===========================================================
                                      .___ __  __   
          _________________  __ __  __| _/|__|/  |_ 
         / ___\_` __ \__  \ |  |  \/ __ | | \\_  __\
        / /_/  >  | \// __ \|  |  / /_/ | |  ||  |  
        \___  /|__|  (____  /____/\____ | |__||__|  
       /_____/            \/           \/           
              grep rough audit - static analysis tool
                  v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
libchado-perl-1.31/soi/README-109-FROM cvterm c, cv
libchado-perl-1.31/soi/README:110:WHERE c.cv_id = cv.cv_id and c.name IN ($top_feature_type) and cv.name = 'so')
libchado-perl-1.31/soi/README-111-UNION
##############################################
libchado-perl-1.31/soi/cgi/get_xml.pl-77-    else {
libchado-perl-1.31/soi/cgi/get_xml.pl:78:        printf STDERR "did not get any feature for %s=%s\n", $type, $cgi->param($type);
libchado-perl-1.31/soi/cgi/get_xml.pl-79-    }
##############################################
libchado-perl-1.31/soi/cgi/get_xml.pl-82-else {
libchado-perl-1.31/soi/cgi/get_xml.pl:83:    printf STDERR "does not support type: %s\n",join(",",$cgi->param());
libchado-perl-1.31/soi/cgi/get_xml.pl-84-}
##############################################
libchado-perl-1.31/soi/scripts/generegion.pl-123-        close(F);
libchado-perl-1.31/soi/scripts/generegion.pl:124:        `xv $tmpf`;
libchado-perl-1.31/soi/scripts/generegion.pl:125:        `rm -f $tmpf`;
libchado-perl-1.31/soi/scripts/generegion.pl-126-    }
##############################################
libchado-perl-1.31/soi/SOI/Adapter.pm-86-        my $so = shift || $ENV{SO_CV_NAME} || 'so';
libchado-perl-1.31/soi/SOI/Adapter.pm:87:        my $hl = $self->_select_hashlist("select cv_id from cv where name = '$so'");
libchado-perl-1.31/soi/SOI/Adapter.pm-88-        unless (@{$hl || []}) {
##############################################
libchado-perl-1.31/soi/SOI/Adapter.pm-136-    my $tlist = join(",",map{sql_q($_)}@$typelist);
libchado-perl-1.31/soi/SOI/Adapter.pm:137:    my $where = $self->_get_where($constr, $opts);
libchado-perl-1.31/soi/SOI/Adapter.pm-138-    my $first_add_w = $where;
##############################################
libchado-perl-1.31/soi/SOI/Adapter.pm-163-    $first_add_w = " AND $first_add_w" if ($first_add_w);
libchado-perl-1.31/soi/SOI/Adapter.pm:164:    my $sec_where = $where;
libchado-perl-1.31/soi/SOI/Adapter.pm-165-    if ($sec_where) {
libchado-perl-1.31/soi/SOI/Adapter.pm:166:        $sec_where = " WHERE $sec_where AND f.is_analysis = 'f'";
libchado-perl-1.31/soi/SOI/Adapter.pm-167-    } else {
##############################################
libchado-perl-1.31/soi/SOI/Adapter.pm-189-           $sp_from
libchado-perl-1.31/soi/SOI/Adapter.pm:190:           WHERE q.name in ($tlist) and cv.name = '$so_cv' and f.is_analysis = 'f' $first_add_w
libchado-perl-1.31/soi/SOI/Adapter.pm-191-          )
##############################################
libchado-perl-1.31/soi/SOI/Adapter.pm-275-
libchado-perl-1.31/soi/SOI/Adapter.pm:276:    my $where = join(" AND ", @{$wheres || []});
libchado-perl-1.31/soi/SOI/Adapter.pm:277:    $where = " WHERE $where" if $where;
libchado-perl-1.31/soi/SOI/Adapter.pm-278-    my $sql =
##############################################
libchado-perl-1.31/soi/SOI/Adapter.pm-371-    my $prog_str = join(",", map{sql_q($_)}@{$progs || []});
libchado-perl-1.31/soi/SOI/Adapter.pm:372:    $where .= " AND an.program IN ($prog_str)" if ($prog_str);
libchado-perl-1.31/soi/SOI/Adapter.pm-373-    my $db_str = join(",", map{sql_q($_)}@{$dbs || []});
libchado-perl-1.31/soi/SOI/Adapter.pm:374:    $where .= " AND an.sourcename IN ($db_str)" if ($db_str);
libchado-perl-1.31/soi/SOI/Adapter.pm-375-
##############################################
libchado-perl-1.31/soi/SOI/Adapter.pm-377-        my $range = $constr->{range};
libchado-perl-1.31/soi/SOI/Adapter.pm:378:        $where .= sprintf(" AND %s", "src.uniquename = ".sql_q($range->{src} || $range->{src_seq}));
libchado-perl-1.31/soi/SOI/Adapter.pm:379:        $where .= sprintf(" AND %s", "fl.fmin <= ".$range->{fmax});
libchado-perl-1.31/soi/SOI/Adapter.pm:380:        $where .= sprintf(" AND %s", "fl.fmax >= ".$range->{fmin});
libchado-perl-1.31/soi/SOI/Adapter.pm-381-        $where .= " AND fl.rank = 0";
##############################################
libchado-perl-1.31/soi/SOI/Adapter.pm-384-        my $src = $constr->{src} || $constr->{src_seq};
libchado-perl-1.31/soi/SOI/Adapter.pm:385:        $where .= sprintf(" AND src.uniquename = %s", sql_q($src)." AND fl.rank = 0");
libchado-perl-1.31/soi/SOI/Adapter.pm-386-    }
##############################################
libchado-perl-1.31/soi/SOI/Adapter.pm-388-        my $src = $constr->{subj} || $constr->{subj_seq};
libchado-perl-1.31/soi/SOI/Adapter.pm:389:        $where .= sprintf(" AND src.uniquename = %s", sql_q($src)." AND fl.rank = 1");
libchado-perl-1.31/soi/SOI/Adapter.pm-390-    }
##############################################
libchado-perl-1.31/soi/SOI/Adapter.pm-417-           cv ON (cv.cv_id = q.cv_id)
libchado-perl-1.31/soi/SOI/Adapter.pm:418:           WHERE cv.name = '$so_cv' AND q.name IN ($tliststr) and $where
libchado-perl-1.31/soi/SOI/Adapter.pm-419-          )
##############################################
libchado-perl-1.31/soi/SOI/Adapter.pm-586-
libchado-perl-1.31/soi/SOI/Adapter.pm:587:    my $where = "(f.name = '$value' OR f.uniquename = '$value')";
libchado-perl-1.31/soi/SOI/Adapter.pm-588-
##############################################
libchado-perl-1.31/soi/SOI/Adapter.pm-605-         cvterm type ON (type.cvterm_id = f.type_id)
libchado-perl-1.31/soi/SOI/Adapter.pm:606:         WHERE type.name = '$type' AND $where
libchado-perl-1.31/soi/SOI/Adapter.pm-607-        );
##############################################
libchado-perl-1.31/soi/SOI/Adapter.pm-699-       INNER join analysis a ON (a.analysis_id = af.analysis_id)
libchado-perl-1.31/soi/SOI/Adapter.pm:700:       WHERE f.name = $band AND cfl.rank = 0 AND a.program = '$prog' AND a.sourcename = '$sn'
libchado-perl-1.31/soi/SOI/Adapter.pm-701-       group by f.name, src);
##############################################
libchado-perl-1.31/soi/SOI/Adapter.pm-863-        confess("Invalid range args $src, $fmin, $fmax") if (!$src || ($fmax-$fmin) <=0);
libchado-perl-1.31/soi/SOI/Adapter.pm:864:        $where = "$src_col = '$src' and $fl_tbl.fmin <= $fmax and $fl_tbl.fmax >= $fmin";
libchado-perl-1.31/soi/SOI/Adapter.pm:865:        $where = "$src_col = '$src' and $fl_tbl.fmin >= $fmin and $fl_tbl.fmax <= $fmax" if ($opts->{within});
libchado-perl-1.31/soi/SOI/Adapter.pm:866:        $where = "$src_col = '$src'" if ($chr_arm);
libchado-perl-1.31/soi/SOI/Adapter.pm-867-    }
##############################################
libchado-perl-1.31/soi/SOI/Adapter.pm-869-        my $src = $constr->{src} || $constr->{src_seq};
libchado-perl-1.31/soi/SOI/Adapter.pm:870:        $where = "$src_col = '$src'";
libchado-perl-1.31/soi/SOI/Adapter.pm-871-    }
##############################################
libchado-perl-1.31/soi/SOI/Adapter.pm-873-        my $src = $constr->{subj} || $constr->{subj_seq};
libchado-perl-1.31/soi/SOI/Adapter.pm:874:        $where = "$src_col = '$src'";
libchado-perl-1.31/soi/SOI/Adapter.pm-875-    }
##############################################
libchado-perl-1.31/soi/SOI/Adapter.pm-895-          FROM cvterm c, cv
libchado-perl-1.31/soi/SOI/Adapter.pm:896:          WHERE c.cv_id = cv.cv_id and c.name IN ($tliststr) and cv.name = '$so_cv')
libchado-perl-1.31/soi/SOI/Adapter.pm-897-         UNION
##############################################
libchado-perl-1.31/soi/SOI/Adapter.pm-981-         );
libchado-perl-1.31/soi/SOI/Adapter.pm:982:    $where = $self->_get_where($constr, $opts);
libchado-perl-1.31/soi/SOI/Adapter.pm-983-    $sql = sprintf("$sql WHERE %s", $where) if ($where);
##############################################
libchado-perl-1.31/modules/phylogeny/functions/phylo.plpgsql-24-    FROM phylonode
libchado-perl-1.31/modules/phylogeny/functions/phylo.plpgsql:25:    WHERE parent_phylonode_id = $1
libchado-perl-1.31/modules/phylogeny/functions/phylo.plpgsql-26-'
##############################################
libchado-perl-1.31/modules/default_schema.sql-1467-  FROM organism
libchado-perl-1.31/modules/default_schema.sql:1468:  WHERE genus=$1
libchado-perl-1.31/modules/default_schema.sql-1469-    AND species=$2
##############################################
libchado-perl-1.31/modules/default_schema.sql-1475-  FROM organism
libchado-perl-1.31/modules/default_schema.sql:1476:  WHERE genus=substring($1,1,position('' '' IN $1)-1)
libchado-perl-1.31/modules/default_schema.sql-1477-    AND species=substring($1,position('' '' IN $1)+1)
##############################################
libchado-perl-1.31/modules/default_schema.sql-1483-  FROM organism
libchado-perl-1.31/modules/default_schema.sql:1484:  WHERE substr(genus,1,1)=substring($1,1,1)
libchado-perl-1.31/modules/default_schema.sql-1485-    AND species=substring($1,position('' '' IN $1)+1)
##############################################
libchado-perl-1.31/modules/default_schema.sql-2385-CREATE OR REPLACE FUNCTION translate_codon(TEXT,BIGINT) RETURNS CHAR AS
libchado-perl-1.31/modules/default_schema.sql:2386: 'SELECT aa FROM genetic_code.gencode_codon_aa WHERE codon=$1 AND gencode_id=$2'
libchado-perl-1.31/modules/default_schema.sql-2387-LANGUAGE 'sql';
##############################################
libchado-perl-1.31/modules/default_schema.sql-2701-  FROM cv INNER JOIN cvterm USING (cv_id)
libchado-perl-1.31/modules/default_schema.sql:2702:  WHERE cvterm.name=$1 AND cv.name=''sequence''
libchado-perl-1.31/modules/default_schema.sql-2703- ' LANGUAGE 'sql';
##############################################
libchado-perl-1.31/modules/default_schema.sql-2708-  FROM cv INNER JOIN cvterm USING (cv_id)
libchado-perl-1.31/modules/default_schema.sql:2709:  WHERE cvterm.name=$1 AND cv.name=''feature_property''
libchado-perl-1.31/modules/default_schema.sql-2710- ' LANGUAGE 'sql';
##############################################
libchado-perl-1.31/modules/default_schema.sql-2715-  FROM cv INNER JOIN cvterm USING (cv_id)
libchado-perl-1.31/modules/default_schema.sql:2716:  WHERE cvterm.name=$1 AND cv.name=''relationship''
libchado-perl-1.31/modules/default_schema.sql-2717- ' LANGUAGE 'sql';
##############################################
libchado-perl-1.31/modules/default_schema.sql-2723-  FROM feature
libchado-perl-1.31/modules/default_schema.sql:2724:  WHERE uniquename=$1
libchado-perl-1.31/modules/default_schema.sql-2725-    AND type_id=get_feature_type_id($2)
##############################################
libchado-perl-1.31/modules/default_schema.sql-2896---- *** eral small cytoplasmic RNA molecules pre ***
libchado-perl-1.31/modules/default_schema.sql:2897:--- *** sent in the cytoplasm and sometimes nucl ***
libchado-perl-1.31/modules/default_schema.sql-2898---- *** eus of a eukaryote.                      ***
##############################################
libchado-perl-1.31/modules/default_schema.sql-37788-    AND g1.group_id = g2.group_id
libchado-perl-1.31/modules/default_schema.sql:37789:    AND g1.srcfeature_id = (SELECT feature_id FROM feature WHERE uniquename = $3)
libchado-perl-1.31/modules/default_schema.sql-37790-    AND boxquery($1, $2) @ boxrange(g1.fmin,g2.fmax)
##############################################
libchado-perl-1.31/modules/default_schema.sql-37795-  FROM groupoverlaps($1,$2,$3)
libchado-perl-1.31/modules/default_schema.sql:37796:  WHERE fmin <= $1 AND fmax >= $2
libchado-perl-1.31/modules/default_schema.sql-37797-' LANGUAGE 'sql';
##############################################
libchado-perl-1.31/modules/default_schema.sql-37801-  FROM groupoverlaps($1,$2,$3)
libchado-perl-1.31/modules/default_schema.sql:37802:  WHERE fmin >= $1 AND fmax <= $2
libchado-perl-1.31/modules/default_schema.sql-37803-' LANGUAGE 'sql';
##############################################
libchado-perl-1.31/modules/default_schema.sql-37807-  FROM groupoverlaps($1,$2,$3)
libchado-perl-1.31/modules/default_schema.sql:37808:  WHERE fmin = $1 AND fmax = $2
libchado-perl-1.31/modules/default_schema.sql-37809-' LANGUAGE 'sql';
##############################################
libchado-perl-1.31/modules/default_schema.sql-39668-    FROM phylonode
libchado-perl-1.31/modules/default_schema.sql:39669:    WHERE parent_phylonode_id = $1
libchado-perl-1.31/modules/default_schema.sql-39670-'
##############################################
libchado-perl-1.31/modules/default_schema.sql-40337-);
libchado-perl-1.31/modules/default_schema.sql:40338:COMMENT ON TABLE stock_relationship_cvterm is 'For germplasm maintenance and pedigree data, stock_relationship. type_id will record cvterms such as "is a female parent of", "a parent for mutation", "is a group_id of", "is a source_id of", etc The cvterms for higher categories such as "generative", "derivative" or "maintenance" can be stored in table stock_relationship_cvterm';
libchado-perl-1.31/modules/default_schema.sql-40339-
##############################################
libchado-perl-1.31/modules/default_schema.sql-42005-FROM cvterm s, feature_cvterm fs
libchado-perl-1.31/modules/default_schema.sql:42006:WHERE fs.feature_id= $1 AND fs.cvterm_id = s.cvterm_id
libchado-perl-1.31/modules/default_schema.sql-42007-UNION
##############################################
libchado-perl-1.31/modules/default_schema.sql-42009-FROM dbxref s, feature_dbxref fs, db d
libchado-perl-1.31/modules/default_schema.sql:42010:WHERE fs.feature_id= $1 AND fs.dbxref_id = s.dbxref_id AND s.db_id = d.db_id
libchado-perl-1.31/modules/default_schema.sql-42011-UNION
##############################################
libchado-perl-1.31/modules/default_schema.sql-42013-FROM synonym s, feature_synonym fs
libchado-perl-1.31/modules/default_schema.sql:42014:WHERE fs.feature_id= $1 AND fs.synonym_id = s.synonym_id
libchado-perl-1.31/modules/default_schema.sql-42015-UNION
##############################################
libchado-perl-1.31/modules/default_schema.sql-42017-FROM featureprop fp, cvterm cv
libchado-perl-1.31/modules/default_schema.sql:42018:WHERE fp.feature_id= $1 AND fp.type_id = cv.cvterm_id 
libchado-perl-1.31/modules/default_schema.sql-42019-UNION
##############################################
libchado-perl-1.31/modules/default_schema.sql-42021-FROM pub s, feature_pub fs
libchado-perl-1.31/modules/default_schema.sql:42022:WHERE fs.feature_id= $1 AND fs.pub_id = s.pub_id
libchado-perl-1.31/modules/default_schema.sql-42023-'
##############################################
libchado-perl-1.31/modules/organism/functions/organism.plpgsql-5-  FROM organism
libchado-perl-1.31/modules/organism/functions/organism.plpgsql:6:  WHERE genus=$1
libchado-perl-1.31/modules/organism/functions/organism.plpgsql-7-    AND species=$2
##############################################
libchado-perl-1.31/modules/organism/functions/organism.plpgsql-13-  FROM organism
libchado-perl-1.31/modules/organism/functions/organism.plpgsql:14:  WHERE genus=substring($1,1,position('' '' IN $1)-1)
libchado-perl-1.31/modules/organism/functions/organism.plpgsql-15-    AND species=substring($1,position('' '' IN $1)+1)
##############################################
libchado-perl-1.31/modules/organism/functions/organism.plpgsql-21-  FROM organism
libchado-perl-1.31/modules/organism/functions/organism.plpgsql:22:  WHERE substr(genus,1,1)=substring($1,1,1)
libchado-perl-1.31/modules/organism/functions/organism.plpgsql-23-    AND species=substring($1,position('' '' IN $1)+1)
##############################################
libchado-perl-1.31/modules/nofuncs.html-19856-	================================================ <br />
libchado-perl-1.31/modules/nofuncs.html:19857:	For germplasm maintenance and pedigree data, stock_relationship. type_id will record cvterms such as "is a female parent of", "a parent for mutation", "is a group_id of", "is a source_id of", etc The cvterms for higher categories such as "generative", "derivative" or "maintenance" can be stored in table stock_relationship_cvterm 
libchado-perl-1.31/modules/nofuncs.html-19858-</em>
##############################################
libchado-perl-1.31/modules/nofuncs.sql-3247-);
libchado-perl-1.31/modules/nofuncs.sql:3248:COMMENT ON TABLE stock_relationship_cvterm is 'For germplasm maintenance and pedigree data, stock_relationship. type_id will record cvterms such as "is a female parent of", "a parent for mutation", "is a group_id of", "is a source_id of", etc The cvterms for higher categories such as "generative", "derivative" or "maintenance" can be stored in table stock_relationship_cvterm';
libchado-perl-1.31/modules/nofuncs.sql-3249-
##############################################
libchado-perl-1.31/modules/default_nofuncs.sql-3247-);
libchado-perl-1.31/modules/default_nofuncs.sql:3248:COMMENT ON TABLE stock_relationship_cvterm is 'For germplasm maintenance and pedigree data, stock_relationship. type_id will record cvterms such as "is a female parent of", "a parent for mutation", "is a group_id of", "is a source_id of", etc The cvterms for higher categories such as "generative", "derivative" or "maintenance" can be stored in table stock_relationship_cvterm';
libchado-perl-1.31/modules/default_nofuncs.sql-3249-
##############################################
libchado-perl-1.31/modules/bin/mk.pl-6-        next if /^\#/;
libchado-perl-1.31/modules/bin/mk.pl:7:        print `cat $_`;
libchado-perl-1.31/modules/bin/mk.pl-8-    }
##############################################
libchado-perl-1.31/modules/sequence/bdgp/bin/create-so-layer.pl-40-if ($help) {
libchado-perl-1.31/modules/sequence/bdgp/bin/create-so-layer.pl:41:    system("perldoc $0");
libchado-perl-1.31/modules/sequence/bdgp/bin/create-so-layer.pl-42-    exit 0;
##############################################
libchado-perl-1.31/modules/sequence/bdgp/bin/create-so-layer.pl-187-    my $from = "INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)";
libchado-perl-1.31/modules/sequence/bdgp/bin/create-so-layer.pl:188:    my $where = "cvterm.name = '$tname'";
libchado-perl-1.31/modules/sequence/bdgp/bin/create-so-layer.pl-189-    my $cmnt = "";
##############################################
libchado-perl-1.31/modules/sequence/bdgp/bin/create-so-layer.pl-191-	$from = "";
libchado-perl-1.31/modules/sequence/bdgp/bin/create-so-layer.pl:192:	$where = "feature.type_id = $type->[0]";
libchado-perl-1.31/modules/sequence/bdgp/bin/create-so-layer.pl-193-	$cmnt = "--- This view is derived from the cvterm database ID.\n".
##############################################
libchado-perl-1.31/modules/sequence/bdgp/bin/create-so-layer.pl-234-        my $pvname = $prefix.'sib_'.$vname;
libchado-perl-1.31/modules/sequence/bdgp/bin/create-so-layer.pl:235:        my $where = $is_consecutive ? "  WHERE fr2.rank - fr1.rank = 1\n" : "";
libchado-perl-1.31/modules/sequence/bdgp/bin/create-so-layer.pl-236-
##############################################
libchado-perl-1.31/modules/sequence/gff-bridge/sequence-gff-funcs.plpgsql-10-FROM cvterm s, feature_cvterm fs
libchado-perl-1.31/modules/sequence/gff-bridge/sequence-gff-funcs.plpgsql:11:WHERE fs.feature_id= $1 AND fs.cvterm_id = s.cvterm_id
libchado-perl-1.31/modules/sequence/gff-bridge/sequence-gff-funcs.plpgsql-12-UNION
##############################################
libchado-perl-1.31/modules/sequence/gff-bridge/sequence-gff-funcs.plpgsql-14-FROM dbxref s, feature_dbxref fs, db d
libchado-perl-1.31/modules/sequence/gff-bridge/sequence-gff-funcs.plpgsql:15:WHERE fs.feature_id= $1 AND fs.dbxref_id = s.dbxref_id AND s.db_id = d.db_id
libchado-perl-1.31/modules/sequence/gff-bridge/sequence-gff-funcs.plpgsql-16-UNION
##############################################
libchado-perl-1.31/modules/sequence/gff-bridge/sequence-gff-funcs.plpgsql-18-FROM synonym s, feature_synonym fs
libchado-perl-1.31/modules/sequence/gff-bridge/sequence-gff-funcs.plpgsql:19:WHERE fs.feature_id= $1 AND fs.synonym_id = s.synonym_id
libchado-perl-1.31/modules/sequence/gff-bridge/sequence-gff-funcs.plpgsql-20-UNION
##############################################
libchado-perl-1.31/modules/sequence/gff-bridge/sequence-gff-funcs.plpgsql-22-FROM featureprop fp, cvterm cv
libchado-perl-1.31/modules/sequence/gff-bridge/sequence-gff-funcs.plpgsql:23:WHERE fp.feature_id= $1 AND fp.type_id = cv.cvterm_id 
libchado-perl-1.31/modules/sequence/gff-bridge/sequence-gff-funcs.plpgsql-24-UNION
##############################################
libchado-perl-1.31/modules/sequence/gff-bridge/sequence-gff-funcs.plpgsql-26-FROM pub s, feature_pub fs
libchado-perl-1.31/modules/sequence/gff-bridge/sequence-gff-funcs.plpgsql:27:WHERE fs.feature_id= $1 AND fs.pub_id = s.pub_id
libchado-perl-1.31/modules/sequence/gff-bridge/sequence-gff-funcs.plpgsql-28-'
##############################################
libchado-perl-1.31/modules/sequence/functions/feature.plpgsql-5-  FROM feature
libchado-perl-1.31/modules/sequence/functions/feature.plpgsql:6:  WHERE uniquename=$1
libchado-perl-1.31/modules/sequence/functions/feature.plpgsql-7-    AND type_id=get_feature_type_id($2)
##############################################
libchado-perl-1.31/modules/sequence/functions/sequtil.plpgsql-60-CREATE OR REPLACE FUNCTION translate_codon(TEXT,BIGINT) RETURNS CHAR AS
libchado-perl-1.31/modules/sequence/functions/sequtil.plpgsql:61: 'SELECT aa FROM genetic_code.gencode_codon_aa WHERE codon=$1 AND gencode_id=$2'
libchado-perl-1.31/modules/sequence/functions/sequtil.plpgsql-62-LANGUAGE 'sql';
##############################################
libchado-perl-1.31/modules/sequence/functions/frange.plpgsql-40-    AND g1.group_id = g2.group_id
libchado-perl-1.31/modules/sequence/functions/frange.plpgsql:41:    AND g1.srcfeature_id = (SELECT feature_id FROM feature WHERE uniquename = $3)
libchado-perl-1.31/modules/sequence/functions/frange.plpgsql-42-    AND boxquery($1, $2) @ boxrange(g1.fmin,g2.fmax)
##############################################
libchado-perl-1.31/modules/sequence/functions/frange.plpgsql-47-  FROM groupoverlaps($1,$2,$3)
libchado-perl-1.31/modules/sequence/functions/frange.plpgsql:48:  WHERE fmin <= $1 AND fmax >= $2
libchado-perl-1.31/modules/sequence/functions/frange.plpgsql-49-' LANGUAGE 'sql';
##############################################
libchado-perl-1.31/modules/sequence/functions/frange.plpgsql-53-  FROM groupoverlaps($1,$2,$3)
libchado-perl-1.31/modules/sequence/functions/frange.plpgsql:54:  WHERE fmin >= $1 AND fmax <= $2
libchado-perl-1.31/modules/sequence/functions/frange.plpgsql-55-' LANGUAGE 'sql';
##############################################
libchado-perl-1.31/modules/sequence/functions/frange.plpgsql-59-  FROM groupoverlaps($1,$2,$3)
libchado-perl-1.31/modules/sequence/functions/frange.plpgsql:60:  WHERE fmin = $1 AND fmax = $2
libchado-perl-1.31/modules/sequence/functions/frange.plpgsql-61-' LANGUAGE 'sql';
##############################################
libchado-perl-1.31/modules/sequence/functions/sequence-cv-helper.plpgsql-12-  FROM cv INNER JOIN cvterm USING (cv_id)
libchado-perl-1.31/modules/sequence/functions/sequence-cv-helper.plpgsql:13:  WHERE cvterm.name=$1 AND cv.name=''sequence''
libchado-perl-1.31/modules/sequence/functions/sequence-cv-helper.plpgsql-14- ' LANGUAGE 'sql';
##############################################
libchado-perl-1.31/modules/sequence/functions/sequence-cv-helper.plpgsql-19-  FROM cv INNER JOIN cvterm USING (cv_id)
libchado-perl-1.31/modules/sequence/functions/sequence-cv-helper.plpgsql:20:  WHERE cvterm.name=$1 AND cv.name=''feature_property''
libchado-perl-1.31/modules/sequence/functions/sequence-cv-helper.plpgsql-21- ' LANGUAGE 'sql';
##############################################
libchado-perl-1.31/modules/sequence/functions/sequence-cv-helper.plpgsql-26-  FROM cv INNER JOIN cvterm USING (cv_id)
libchado-perl-1.31/modules/sequence/functions/sequence-cv-helper.plpgsql:27:  WHERE cvterm.name=$1 AND cv.name=''relationship''
libchado-perl-1.31/modules/sequence/functions/sequence-cv-helper.plpgsql-28- ' LANGUAGE 'sql';
##############################################
libchado-perl-1.31/modules/sequence/apollo-bridge/insert_ad_doc_cv.pl-20-            my $cvterm = $1;
libchado-perl-1.31/modules/sequence/apollo-bridge/insert_ad_doc_cv.pl:21:            print INSERTS "INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), '$cv:$cvterm');\n";
libchado-perl-1.31/modules/sequence/apollo-bridge/insert_ad_doc_cv.pl:22:            print INSERTS "INSERT INTO cvterm (cv_id,name,dbxref_id,is_relationshiptype) VALUES ((select cv_id from cv where name='$cv'),'$cvterm',(select dbxref_id from dbxref where accession='$cv:$cvterm'),1);\n";
libchado-perl-1.31/modules/sequence/apollo-bridge/insert_ad_doc_cv.pl-23-        } else {
libchado-perl-1.31/modules/sequence/apollo-bridge/insert_ad_doc_cv.pl-24-            my $cvterm = $term;
libchado-perl-1.31/modules/sequence/apollo-bridge/insert_ad_doc_cv.pl:25:            print INSERTS "INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), '$cv:$cvterm');\n";
libchado-perl-1.31/modules/sequence/apollo-bridge/insert_ad_doc_cv.pl:26:            print INSERTS "INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='$cv'),'$cvterm',(select dbxref_id from dbxref where accession='$cv:$cvterm'));\n";
libchado-perl-1.31/modules/sequence/apollo-bridge/insert_ad_doc_cv.pl-27-        }
##############################################
libchado-perl-1.31/modules/sequence/bridges/so_bridge.sql-169---- *** eral small cytoplasmic RNA molecules pre ***
libchado-perl-1.31/modules/sequence/bridges/so_bridge.sql:170:--- *** sent in the cytoplasm and sometimes nucl ***
libchado-perl-1.31/modules/sequence/bridges/so_bridge.sql-171---- *** eus of a eukaryote.                      ***
##############################################
libchado-perl-1.31/modules/sequence/bridges/so-bridge.sql-169---- *** eral small cytoplasmic RNA molecules pre ***
libchado-perl-1.31/modules/sequence/bridges/so-bridge.sql:170:--- *** sent in the cytoplasm and sometimes nucl ***
libchado-perl-1.31/modules/sequence/bridges/so-bridge.sql-171---- *** eus of a eukaryote.                      ***
##############################################
libchado-perl-1.31/modules/sequence/bridges/bin/create-sofa-bridge.pl-44-if ($help) {
libchado-perl-1.31/modules/sequence/bridges/bin/create-sofa-bridge.pl:45:    system("perldoc $0");
libchado-perl-1.31/modules/sequence/bridges/bin/create-sofa-bridge.pl-46-    exit 0;
##############################################
libchado-perl-1.31/modules/sequence/bridges/bin/create-sofa-bridge.pl-160-    my $from = "INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)";
libchado-perl-1.31/modules/sequence/bridges/bin/create-sofa-bridge.pl:161:    my $where = "cvterm.name = '$tname'";
libchado-perl-1.31/modules/sequence/bridges/bin/create-sofa-bridge.pl-162-    if ($id_based) {
libchado-perl-1.31/modules/sequence/bridges/bin/create-sofa-bridge.pl-163-        my $id = $n2id{$tname};        
libchado-perl-1.31/modules/sequence/bridges/bin/create-sofa-bridge.pl:164:        $where = "feature.type_id = $id";
libchado-perl-1.31/modules/sequence/bridges/bin/create-sofa-bridge.pl-165-    }
##############################################
libchado-perl-1.31/modules/sequence/bridges/sofa-bridge.sql-2141---- *** Any one of several small cytoplasmic RNA ***
libchado-perl-1.31/modules/sequence/bridges/sofa-bridge.sql:2142:--- ***  moleculespresent in the cytoplasm and s ***
libchado-perl-1.31/modules/sequence/bridges/sofa-bridge.sql-2143---- *** ometimes nucleus of a eukaryote.         ***
##############################################
libchado-perl-1.31/modules/stock/stock.sql-154-);
libchado-perl-1.31/modules/stock/stock.sql:155:COMMENT ON TABLE stock_relationship_cvterm is 'For germplasm maintenance and pedigree data, stock_relationship. type_id will record cvterms such as "is a female parent of", "a parent for mutation", "is a group_id of", "is a source_id of", etc The cvterms for higher categories such as "generative", "derivative" or "maintenance" can be stored in table stock_relationship_cvterm';
libchado-perl-1.31/modules/stock/stock.sql-156-
##############################################
libchado-perl-1.31/modules/stock/stock.html-1049-	================================================ <br />
libchado-perl-1.31/modules/stock/stock.html:1050:	For germplasm maintenance and pedigree data, stock_relationship. type_id will record cvterms such as "is a female parent of", "a parent for mutation", "is a group_id of", "is a source_id of", etc The cvterms for higher categories such as "generative", "derivative" or "maintenance" can be stored in table stock_relationship_cvterm 
libchado-perl-1.31/modules/stock/stock.html-1051-</em>
##############################################
libchado-perl-1.31/conf/bulkfiles/chadofeatsql.xml-220-    FROM   feature feat, cvterm featcv, cv socv
libchado-perl-1.31/conf/bulkfiles/chadofeatsql.xml:221:    WHERE  socv.name = '${seq_ontology}'
libchado-perl-1.31/conf/bulkfiles/chadofeatsql.xml-222-       and featcv.cv_id = socv.cv_id 
##############################################
libchado-perl-1.31/install_util/src_install.PLS-57-chmod 0755, $file or die "Can't reset permissions for $file: $!\n";
libchado-perl-1.31/install_util/src_install.PLS:58:exec("$Config{'eunicefix'} $file") if $Config{'eunicefix'} ne ':';
libchado-perl-1.31/install_util/src_install.PLS-59-chdir $origdir;
##############################################
libchado-perl-1.31/install_util/conf_install.PLS-89-chmod 0755, $file or die "Can't reset permissions for $file: $!\n";
libchado-perl-1.31/install_util/conf_install.PLS:90:exec("$Config{'eunicefix'} $file") if $Config{'eunicefix'} ne ':';
libchado-perl-1.31/install_util/conf_install.PLS-91-chdir $origdir;
##############################################
libchado-perl-1.31/bin/gmod_chado_properties.pl-54-    'dbprofile=s'   => \$DBPROFILE,
libchado-perl-1.31/bin/gmod_chado_properties.pl:55:) or ( system( 'pod2text', $0 ), exit -1 );
libchado-perl-1.31/bin/gmod_chado_properties.pl-56-
##############################################
libchado-perl-1.31/bin/gmod_chado_properties.pl-130-                #there is a version in there, update it
libchado-perl-1.31/bin/gmod_chado_properties.pl:131:                my $update_query = "UPDATE chadoprop SET value = $version WHERE type_id = $cvterm_id";
libchado-perl-1.31/bin/gmod_chado_properties.pl-132-                $dbh->do($update_query);
##############################################
libchado-perl-1.31/bin/gmod_gff2biomart5.pl-378--- LOAD DATA INFILE '$fullpath$maintab.xml' INTO TABLE tmpxml LINES TERMINATED BY '~';
libchado-perl-1.31/bin/gmod_gff2biomart5.pl:379:-- UPDATE meta_configuration set xml = (select xml from tmpxml) where datasetID = $mainid;
libchado-perl-1.31/bin/gmod_gff2biomart5.pl-380--- TRUNCATE table tmpxml;
libchado-perl-1.31/bin/gmod_gff2biomart5.pl-381--- LOAD DATA INFILE '$fullpath$dnatab.xml' INTO TABLE tmpxml LINES TERMINATED BY '~';
libchado-perl-1.31/bin/gmod_gff2biomart5.pl:382:-- UPDATE meta_configuration set xml = (select xml from tmpxml) where datasetID = $dnaid;
libchado-perl-1.31/bin/gmod_gff2biomart5.pl-383--- DROP TABLE tmpxml;
##############################################
libchado-perl-1.31/bin/gmod_fasta2gff3.pl-16-    'nosequence'     => \$NOSEQUENCE,
libchado-perl-1.31/bin/gmod_fasta2gff3.pl:17:  ) or ( system( 'pod2text', $0 ), exit -1 );
libchado-perl-1.31/bin/gmod_fasta2gff3.pl-18-
##############################################
libchado-perl-1.31/bin/test_load.pl-31-        print "Dropping database '$dbname'\n";
libchado-perl-1.31/bin/test_load.pl:32:        system( "dropdb $dbname" ) == 0 or die "Cannot drop database: $?";
libchado-perl-1.31/bin/test_load.pl-33-    }
##############################################
libchado-perl-1.31/bin/test_load.pl-40-print "Creating new database called '$dbname'\n";
libchado-perl-1.31/bin/test_load.pl:41:system( "createdb $dbname" ) == 0 or die "Cannot create database: $?";
libchado-perl-1.31/bin/test_load.pl-42-
##############################################
libchado-perl-1.31/bin/make_cvtermpath.pl-42-my $cv_id;
libchado-perl-1.31/bin/make_cvtermpath.pl:43:warn "select cv_id from cv where name = '$cvname'";
libchado-perl-1.31/bin/make_cvtermpath.pl:44:my $sth_cv = $db->prepare("select cv_id from cv where name = '$cvname'");
libchado-perl-1.31/bin/make_cvtermpath.pl-45-$sth_cv->execute;
##############################################
libchado-perl-1.31/bin/make_cvtermpath.pl-53-
libchado-perl-1.31/bin/make_cvtermpath.pl:54:my $sth_cvterm_relationship = $db->prepare("select subject_id,type_id,object_id from cvterm_relationship,cvterm where cvterm_relationship.subject_id = cvterm.cvterm_id and cvterm.cv_id = $cv_id");
libchado-perl-1.31/bin/make_cvtermpath.pl-55-$sth_cvterm_relationship->execute;
##############################################
libchado-perl-1.31/bin/make_cvtermpath.pl-119-		print "insert into cvtermpath (subject_id,object_id,type_id,cv_id,pathdistance) values
libchado-perl-1.31/bin/make_cvtermpath.pl:120:                                      ($s,$object,(select cvterm_id from cvterm where name = 'OBO_REL:0001'),$cv_id,$tdist);\n";
libchado-perl-1.31/bin/make_cvtermpath.pl-121-		print "insert into cvtermpath (subject_id,object_id,type_id,cv_id,pathdistance) values
libchado-perl-1.31/bin/make_cvtermpath.pl:122:                                      ($object,$subject,(select cvterm_id from cvterm where name = 'OBO_REL:0001'),$cv_id,-$tdist);\n";
libchado-perl-1.31/bin/make_cvtermpath.pl-123-	  }
##############################################
libchado-perl-1.31/bin/chado-build-schema.pl-23-if ($HELP) {
libchado-perl-1.31/bin/chado-build-schema.pl:24:    system ("pod2text", $0);
libchado-perl-1.31/bin/chado-build-schema.pl-25-    exit(0);
##############################################
libchado-perl-1.31/bin/chado-build-schema.pl-218-        $fh->close;
libchado-perl-1.31/bin/chado-build-schema.pl:219:        #print `cat $SCHEMA_FILE`;
libchado-perl-1.31/bin/chado-build-schema.pl-220-        $mw->messageBox(-message=>"Pg schema created in file $SCHEMA_FILE");
##############################################
libchado-perl-1.31/bin/chado-build-schema.pl-297-sub usage {
libchado-perl-1.31/bin/chado-build-schema.pl:298:    system( 'pod2usage', $0 );
libchado-perl-1.31/bin/chado-build-schema.pl-299-    exit(0);
##############################################
libchado-perl-1.31/bin/make_partial_indexes.pl-18-  $dbh->do("create index featureloc_src_$id on featureloc (fmin,fmax)
libchado-perl-1.31/bin/make_partial_indexes.pl:19:            where srcfeature_id = $id");  
libchado-perl-1.31/bin/make_partial_indexes.pl-20-}
##############################################
libchado-perl-1.31/bin/config.PLS-77-  'database:s'      => \$DATABASE,
libchado-perl-1.31/bin/config.PLS:78:) or ( system ('pod2text', $0), exit -1);
libchado-perl-1.31/bin/config.PLS-79-
##############################################
libchado-perl-1.31/bin/gmod_update_chado.pl-43-    'dbprofile=s'   => \$DBPROFILE,
libchado-perl-1.31/bin/gmod_update_chado.pl:44:) or ( system( 'pod2text', $0 ), exit -1 );
libchado-perl-1.31/bin/gmod_update_chado.pl-45-
##############################################
libchado-perl-1.31/bin/gmod_update_chado.pl-53-
libchado-perl-1.31/bin/gmod_update_chado.pl:54:my $current_version = `gmod_chado_properties.pl --version --dbprof $DBPROFILE`;
libchado-perl-1.31/bin/gmod_update_chado.pl-55-chomp $current_version;
##############################################
libchado-perl-1.31/bin/gmod_update_chado.pl-87-
libchado-perl-1.31/bin/gmod_update_chado.pl:88:system("cp $path $cwd");
libchado-perl-1.31/bin/gmod_update_chado.pl-89-unless ($schema eq 'public') {
libchado-perl-1.31/bin/gmod_update_chado.pl:90:    system("perl -pi -e 's/public/$schema/g' diff.sql");
libchado-perl-1.31/bin/gmod_update_chado.pl-91-}
##############################################
libchado-perl-1.31/bin/gmod_update_chado.pl-93-my $syscommand = "cat diff.sql | psql -U $dbuser -p $dbport -h $dbhost $dbname";
libchado-perl-1.31/bin/gmod_update_chado.pl:94:system($syscommand) == 0 or die "failed updating database";
libchado-perl-1.31/bin/gmod_update_chado.pl-95-
libchado-perl-1.31/bin/gmod_update_chado.pl-96-#now update the schema version in the chadoprop table
libchado-perl-1.31/bin/gmod_update_chado.pl:97:system("gmod_chado_properties.pl --version $version --force --dbprof $DBPROFILE");
libchado-perl-1.31/bin/gmod_update_chado.pl-98-
##############################################
libchado-perl-1.31/bin/gmod_dump_gff3.pl-88-unless ($organism_id) {
libchado-perl-1.31/bin/gmod_dump_gff3.pl:89:    system( 'pod2text', $0 );
libchado-perl-1.31/bin/gmod_dump_gff3.pl-90-    warn "Organism:$ORGANISM not found in database\n";
##############################################
libchado-perl-1.31/bin/gmod_add_organism.pl-66-    'dbprofile=s'   => \$DBPROFILE,
libchado-perl-1.31/bin/gmod_add_organism.pl:67:) or ( system( 'pod2text', $0 ), exit -1 );
libchado-perl-1.31/bin/gmod_add_organism.pl-68-
##############################################
libchado-perl-1.31/bin/gmod_extract_dbxref_from_gff.pl-51-if ($ARGV[0] =~ /-h/) {
libchado-perl-1.31/bin/gmod_extract_dbxref_from_gff.pl:52:    system( 'pod2text', $0);
libchado-perl-1.31/bin/gmod_extract_dbxref_from_gff.pl-53-    exit -1;
##############################################
libchado-perl-1.31/bin/AutoDBI.PL-128-chmod 0755, $file or die "Can't reset permissions for $file: $!\n";
libchado-perl-1.31/bin/AutoDBI.PL:129:exec("$Config{'eunicefix'} $file") if $Config{'eunicefix'} ne ':';
##############################################
libchado-perl-1.31/bin/create-so-bridge.pl-51-if ($help) {
libchado-perl-1.31/bin/create-so-bridge.pl:52:    system("perldoc $0");
libchado-perl-1.31/bin/create-so-bridge.pl-53-    exit 0;
##############################################
libchado-perl-1.31/bin/create-so-bridge.pl-127-        $dbh->selectall_arrayref("SELECT DISTINCT cvterm_id, cvterm.name
libchado-perl-1.31/bin/create-so-bridge.pl:128:	   FROM cvterm INNER JOIN cv USING (cv_id) WHERE cv.name='$ontology'");
libchado-perl-1.31/bin/create-so-bridge.pl-129-    }
##############################################
libchado-perl-1.31/bin/create-so-bridge.pl-142-          FROM cvterm INNER JOIN feature_cvterm USING (cvterm_id)
libchado-perl-1.31/bin/create-so-bridge.pl:143:          WHERE cv_id IN (SELECT cv_id FROM cv WHERE name = '$ontology'");
libchado-perl-1.31/bin/create-so-bridge.pl-144-    }
##############################################
libchado-perl-1.31/bin/create-so-bridge.pl-227-    }
libchado-perl-1.31/bin/create-so-bridge.pl:228:    my $where = "cvterm.name = '$tname'";
libchado-perl-1.31/bin/create-so-bridge.pl-229-    if ($id_based and $ontology eq 'sequence') {
libchado-perl-1.31/bin/create-so-bridge.pl-230-        my $id = $n2id{$tname};        
libchado-perl-1.31/bin/create-so-bridge.pl:231:        $where = "feature.type_id = $id";
libchado-perl-1.31/bin/create-so-bridge.pl-232-    }
##############################################
libchado-perl-1.31/bin/gmod_sort_gff3.pl-11-    'outfile=s'    => \$OUTFILE,
libchado-perl-1.31/bin/gmod_sort_gff3.pl:12:  ) or ( system( 'pod2text', $0 ), exit -1 );
libchado-perl-1.31/bin/gmod_sort_gff3.pl-13-
##############################################
libchado-perl-1.31/bin/gmod_apollo_triggers.pl-68-
libchado-perl-1.31/bin/gmod_apollo_triggers.pl:69:    system ("cat $gmod_root/src/chado/modules/sequence/apollo-bridge/ontology_inserts.sql | psql $dbname");
libchado-perl-1.31/bin/gmod_apollo_triggers.pl-70-
libchado-perl-1.31/bin/gmod_apollo_triggers.pl:71:    system ("cat $gmod_root/src/chado/modules/sequence/apollo-bridge/apollo.inserts | psql $dbname");
libchado-perl-1.31/bin/gmod_apollo_triggers.pl-72-
libchado-perl-1.31/bin/gmod_apollo_triggers.pl:73:    system ("cat $gmod_root/src/chado/modules/sequence/apollo-bridge/apollo-triggers.plpgsql | psql $dbname");
libchado-perl-1.31/bin/gmod_apollo_triggers.pl-74-
##############################################
libchado-perl-1.31/bin/chado-fix-flybase-instance.pl-90-        my $cmd = "go2chadoxml $path > $outf";
libchado-perl-1.31/bin/chado-fix-flybase-instance.pl:91:        system($cmd) && die("problem with: $cmd");
libchado-perl-1.31/bin/chado-fix-flybase-instance.pl-92-        my $chadonode = Data::Stag->parse($outf);
##############################################
libchado-perl-1.31/bin/chado-fix-flybase-instance.pl-112-      selectcol("SELECT DISTINCT cvterm_id FROM cvterm INNER JOIN cv USING (cv_id) WHERE cv.name='sequence' AND cvterm.name='match_part'");
libchado-perl-1.31/bin/chado-fix-flybase-instance.pl:113:    dosql("UPDATE feature SET type_id = $match_part_id WHERE type_id = $match_id AND feature_id IN (SELECT subject_id FROM feature_relationship)");
libchado-perl-1.31/bin/chado-fix-flybase-instance.pl-114-}
##############################################
libchado-perl-1.31/bin/chado-fix-flybase-instance.pl-183-    my $rows =
libchado-perl-1.31/bin/chado-fix-flybase-instance.pl:184:      selectall("SELECT DISTINCT t2.cvterm_id, t.cvterm_id FROM $table AS x INNER JOIN cvterm AS t ON (x.$col = t.cvterm_id) INNER JOIN cvterm AS t2 ON (t.name=t2.name) INNER JOIN cv ON (cv.cv_id = t2.cv_id) WHERE cv.name='$cv' AND t.cv_id != cv.cv_id");
libchado-perl-1.31/bin/chado-fix-flybase-instance.pl-185-
##############################################
libchado-perl-1.31/bin/chado-fix-flybase-instance.pl-194-	print STDERR "mapping $old_cvterm_id to $cvterm_id\n";
libchado-perl-1.31/bin/chado-fix-flybase-instance.pl:195:	$dbh->do("UPDATE feature SET type_id = $cvterm_id WHERE type_id=$old_cvterm_id");
libchado-perl-1.31/bin/chado-fix-flybase-instance.pl-196-        print STDERR "Done!\n";
libchado-perl-1.31/bin/chado-fix-flybase-instance.pl:197:	#print "UPDATE feature SET type_id = $cvterm_id WHERE type_id=$old_cvterm_id\n";
libchado-perl-1.31/bin/chado-fix-flybase-instance.pl-198-    }
##############################################
libchado-perl-1.31/bin/chado-fix-flybase-instance.pl-207-        my $rows =
libchado-perl-1.31/bin/chado-fix-flybase-instance.pl:208:          selectall("SELECT DISTINCT cvterm_id FROM cvterm INNER JOIN cv USING (cv_id) WHERE cv.name!='$cv' AND cvterm.name='$from'");
libchado-perl-1.31/bin/chado-fix-flybase-instance.pl-209-        return unless @$rows; # done already
##############################################
libchado-perl-1.31/bin/chado-fix-flybase-instance.pl-214-        $rows =
libchado-perl-1.31/bin/chado-fix-flybase-instance.pl:215:          selectall("SELECT DISTINCT cvterm_id FROM cvterm INNER JOIN cv USING (cv_id) WHERE cv.name='$cv' AND cvterm.name='$to'");
libchado-perl-1.31/bin/chado-fix-flybase-instance.pl-216-        if (@$rows != 1) {
##############################################
libchado-perl-1.31/bin/chado-fix-flybase-instance.pl-221-        print STDERR "map $old_type_id to $new_type_id in $table.$col\n";
libchado-perl-1.31/bin/chado-fix-flybase-instance.pl:222:        $dbh->do("UPDATE $table SET $col = $new_type_id WHERE $col=$old_type_id");
libchado-perl-1.31/bin/chado-fix-flybase-instance.pl-223-        print STDERR "Done!\n";
##############################################
libchado-perl-1.31/bin/gmod_gff3_preprocessor.pl-92-    'inheritance_tiers=i' => \$INHERITANCE_TIERS,
libchado-perl-1.31/bin/gmod_gff3_preprocessor.pl:93:) or ( system( 'pod2text', $0 ), exit -1 );
libchado-perl-1.31/bin/gmod_gff3_preprocessor.pl-94-
##############################################
libchado-perl-1.31/bin/gmod_materialized_view_tool.pl-222-    'help'            => \$HELP,
libchado-perl-1.31/bin/gmod_materialized_view_tool.pl:223:) or ( system( 'pod2text', $0 ), exit -1 );
libchado-perl-1.31/bin/gmod_materialized_view_tool.pl-224-
libchado-perl-1.31/bin/gmod_materialized_view_tool.pl:225:( system( 'pod2text', $0 ), exit -1 ) if $HELP;
libchado-perl-1.31/bin/gmod_materialized_view_tool.pl-226-
##############################################
libchado-perl-1.31/bin/gmod_materialized_view_tool.pl-289-else {
libchado-perl-1.31/bin/gmod_materialized_view_tool.pl:290:    system( 'pod2text', $0 ), exit -1;
libchado-perl-1.31/bin/gmod_materialized_view_tool.pl-291-}
##############################################
libchado-perl-1.31/bin/gmod_make_cvtermpath.pl-187-my $cv_id;
libchado-perl-1.31/bin/gmod_make_cvtermpath.pl:188:warn "select cv_id from cv where name = '$cvname'" if $verbose;
libchado-perl-1.31/bin/gmod_make_cvtermpath.pl:189:my $sth_cv = $db->prepare("select cv_id from cv where name = '$cvname'");
libchado-perl-1.31/bin/gmod_make_cvtermpath.pl-190-$sth_cv->execute;
##############################################
libchado-perl-1.31/bin/gmod_make_cvtermpath.pl-202-
libchado-perl-1.31/bin/gmod_make_cvtermpath.pl:203:my $sth_cvterm_relationship = $db->prepare("select subject_id,type_id,object_id from cvterm_relationship,cvterm where cvterm_relationship.subject_id = cvterm.cvterm_id and cvterm.cv_id = $cv_id");
libchado-perl-1.31/bin/gmod_make_cvtermpath.pl-204-$sth_cvterm_relationship->execute;
##############################################
libchado-perl-1.31/lib/Bio/Chado/Builder.pm-89-
libchado-perl-1.31/lib/Bio/Chado/Builder.pm:90:  system( $sys_call ) == 0 or croak "Error executing '$sys_call': $?";
libchado-perl-1.31/lib/Bio/Chado/Builder.pm-91-
##############################################
libchado-perl-1.31/lib/Bio/Chado/Builder.pm-96-  if ($db_org and $db_org ne 'none' and ref $db_org ne 'HASH') {
libchado-perl-1.31/lib/Bio/Chado/Builder.pm:97:      my $result = `bin/gmod_add_organism.pl --name_only --common_name $db_org`;
libchado-perl-1.31/lib/Bio/Chado/Builder.pm-98-      unless ($result) {
libchado-perl-1.31/lib/Bio/Chado/Builder.pm-99-          print "Adding $db_org to the database...\n";
libchado-perl-1.31/lib/Bio/Chado/Builder.pm:100:          system('/usr/share/gmod/chado/bin/gmod_add_organism.pl','--common_name',$db_org);
libchado-perl-1.31/lib/Bio/Chado/Builder.pm-101-      }  
##############################################
libchado-perl-1.31/lib/Bio/Chado/Builder.pm-104-  #set the chado schema version in the database
libchado-perl-1.31/lib/Bio/Chado/Builder.pm:105:  system("/usr/share/gmod/chado/bin/gmod_chado_properties.pl --dbprofile $db_name --force --version $schema_version"); 
libchado-perl-1.31/lib/Bio/Chado/Builder.pm-106-
##############################################
libchado-perl-1.31/lib/Bio/Chado/Builder.pm-131-
libchado-perl-1.31/lib/Bio/Chado/Builder.pm:132:  my $version = `gmod_chado_properties.pl --dbprofile $db_name --version`; 
libchado-perl-1.31/lib/Bio/Chado/Builder.pm-133-  chomp $version;
##############################################
libchado-perl-1.31/lib/Bio/Chado/Builder.pm-136-    print "Attempting schema update.\n";
libchado-perl-1.31/lib/Bio/Chado/Builder.pm:137:    system("/usr/share/gmod/chado/bin/gmod_update_chado.pl --dbprofile $db_name");
libchado-perl-1.31/lib/Bio/Chado/Builder.pm-138-  } 
##############################################
libchado-perl-1.31/lib/Bio/Chado/Builder.pm-220-
libchado-perl-1.31/lib/Bio/Chado/Builder.pm:221:      my $result = system( $sys_call );
libchado-perl-1.31/lib/Bio/Chado/Builder.pm-222-      if ( $result != 0 ) { 
##############################################
libchado-perl-1.31/lib/Bio/Chado/Builder.pm-345-
libchado-perl-1.31/lib/Bio/Chado/Builder.pm:346:      my $result = system( $sys_call );
libchado-perl-1.31/lib/Bio/Chado/Builder.pm-347-
##############################################
libchado-perl-1.31/lib/Bio/Chado/Builder.pm-363-
libchado-perl-1.31/lib/Bio/Chado/Builder.pm:364:      $result = system( $sys_call );
libchado-perl-1.31/lib/Bio/Chado/Builder.pm-365-
##############################################
libchado-perl-1.31/lib/Bio/Chado/Builder.pm-381-
libchado-perl-1.31/lib/Bio/Chado/Builder.pm:382:        $result = system( $sys_call );
libchado-perl-1.31/lib/Bio/Chado/Builder.pm-383-
##############################################
libchado-perl-1.31/lib/Bio/Chado/Builder.pm-400-
libchado-perl-1.31/lib/Bio/Chado/Builder.pm:401:        $result = system( $sys_call );
libchado-perl-1.31/lib/Bio/Chado/Builder.pm-402-
##############################################
libchado-perl-1.31/lib/Bio/Chado/Builder.pm-504-
libchado-perl-1.31/lib/Bio/Chado/Builder.pm:505:        my $result = system( $sys_call );
libchado-perl-1.31/lib/Bio/Chado/Builder.pm-506-
##############################################
libchado-perl-1.31/lib/Bio/GMOD/DB/Adapter/Wormbase.pm-29-      
libchado-perl-1.31/lib/Bio/GMOD/DB/Adapter/Wormbase.pm:30:        my $sth = $self->dbh->prepare("SELECT cv_id FROM cv WHERE name='". $self->fp_cv()  ."'");
libchado-perl-1.31/lib/Bio/GMOD/DB/Adapter/Wormbase.pm-31-          # dgg: dropped  'autocreated' due to SO/auto conflicts for things like 'gene', 'chromosome'
##############################################
libchado-perl-1.31/lib/Bio/GMOD/DB/Adapter/Wormbase.pm-45-#       if (!$self->{const}{tried_fp_cv} and !$self->{const}{fp_cv_id}) {
libchado-perl-1.31/lib/Bio/GMOD/DB/Adapter/Wormbase.pm:46:#         my $sth = $self->dbh->prepare("SELECT cv_id FROM cv WHERE name='". $self->fp_cv  ."'");
libchado-perl-1.31/lib/Bio/GMOD/DB/Adapter/Wormbase.pm-47-#         $sth->execute;
##############################################
libchado-perl-1.31/lib/Bio/GMOD/DB/Adapter.pm-2525-  INSERT INTO dbxref (db_id,accession)
libchado-perl-1.31/lib/Bio/GMOD/DB/Adapter.pm:2526:    VALUES ((select db_id from db where name='null'),'autocreated:$tag');
libchado-perl-1.31/lib/Bio/GMOD/DB/Adapter.pm-2527-  INSERT INTO cvterm (cv_id,name,dbxref_id)
libchado-perl-1.31/lib/Bio/GMOD/DB/Adapter.pm:2528:    VALUES ((select cv_id from cv where name='autocreated'), '$tag',
libchado-perl-1.31/lib/Bio/GMOD/DB/Adapter.pm:2529:            (select dbxref_id from dbxref where accession='autocreated:$tag'));
libchado-perl-1.31/lib/Bio/GMOD/DB/Adapter.pm-2530-
##############################################
libchado-perl-1.31/lib/Bio/GMOD/DB/Adapter.pm-2547-  my $fh = $self->file_handles('delete');
libchado-perl-1.31/lib/Bio/GMOD/DB/Adapter.pm:2548:  print $fh "DELETE FROM $table WHERE feature_id = $feature_id;\n";
libchado-perl-1.31/lib/Bio/GMOD/DB/Adapter.pm-2549-  return;
##############################################
libchado-perl-1.31/lib/Bio/GMOD/DB/Adapter.pm-2578-  my $len = length($string);
libchado-perl-1.31/lib/Bio/GMOD/DB/Adapter.pm:2579:  print $fh "UPDATE feature set residues='$string', seqlen=$len WHERE feature_id=$feature_id;\n";
libchado-perl-1.31/lib/Bio/GMOD/DB/Adapter.pm-2580-
##############################################
libchado-perl-1.31/lib/Bio/GMOD/DB/Adapter.pm-2613-  my $len = length($string);
libchado-perl-1.31/lib/Bio/GMOD/DB/Adapter.pm:2614:  print $fh "UPDATE feature set residues='$string',seqlen=$len WHERE feature_id=$feature_id;\n";
libchado-perl-1.31/lib/Bio/GMOD/DB/Adapter.pm-2615-
##############################################
libchado-perl-1.31/lib/Bio/GMOD/DB/Adapter.pm-3797-      
libchado-perl-1.31/lib/Bio/GMOD/DB/Adapter.pm:3798:        my $sth = $self->dbh->prepare("SELECT cv_id FROM cv WHERE name='". $self->fp_cv()  ."'");
libchado-perl-1.31/lib/Bio/GMOD/DB/Adapter.pm-3799-          # dgg: dropped  'autocreated' due to SO/auto conflicts for things like 'gene', 'chromosome'
##############################################
libchado-perl-1.31/lib/Bio/GMOD/DB/Adapter.pm-3813-#       if (!$self->{const}{tried_fp_cv} and !$self->{const}{fp_cv_id}) {
libchado-perl-1.31/lib/Bio/GMOD/DB/Adapter.pm:3814:#         my $sth = $self->dbh->prepare("SELECT cv_id FROM cv WHERE name='". $self->fp_cv  ."'");
libchado-perl-1.31/lib/Bio/GMOD/DB/Adapter.pm-3815-#         $sth->execute;
##############################################
libchado-perl-1.31/lib/Bio/GMOD/DB/Adapter.pm-4737-
libchado-perl-1.31/lib/Bio/GMOD/DB/Adapter.pm:4738:    my $sth  = $dbh->prepare("SELECT distinct gffline FROM gff_sort_tmp WHERE refseq = id") or $self->throw();
libchado-perl-1.31/lib/Bio/GMOD/DB/Adapter.pm-4739-    $sth->execute or $self->throw();
##############################################
libchado-perl-1.31/lib/Bio/GMOD/DB/Adapter.pm-4758-
libchado-perl-1.31/lib/Bio/GMOD/DB/Adapter.pm:4759:    $sth  = $dbh->prepare("SELECT distinct gffline,id FROM gff_sort_tmp WHERE parent is null and refseq != id order by id") or $self->throw();
libchado-perl-1.31/lib/Bio/GMOD/DB/Adapter.pm-4760-    $sth->execute or $self->throw();
##############################################
libchado-perl-1.31/lib/Bio/GMOD/Bulkfiles.pm-751-    #$arm =~ s/$from/$to/g;
libchado-perl-1.31/lib/Bio/GMOD/Bulkfiles.pm:752:    if ($to =~ /\$/) { $arm =~ s/$from/eval($to)/e; }
libchado-perl-1.31/lib/Bio/GMOD/Bulkfiles.pm-753-    else { $arm =~ s/$from/$to/g; }
##############################################
libchado-perl-1.31/lib/Bio/GMOD/Bulkfiles.pm-1160-      foreach my $fs (@$fileset) {
libchado-perl-1.31/lib/Bio/GMOD/Bulkfiles.pm:1161:        system("gzip -f ".$fs->{path}) if (-e $fs->{path} && $fs->{path} !~ /\.gz$/);
libchado-perl-1.31/lib/Bio/GMOD/Bulkfiles.pm-1162-        }
##############################################
libchado-perl-1.31/lib/Bio/GMOD/Bulkfiles.pm-1248-    my $cmd="cat $path | $sortfeaturescmd > $path.new";
libchado-perl-1.31/lib/Bio/GMOD/Bulkfiles.pm:1249:    if (system($cmd) == 0) { rename("$path.new",$path); $finfo->{dosort}= 0; }
libchado-perl-1.31/lib/Bio/GMOD/Bulkfiles.pm-1250-    else { my $err= $? >> 8; warn "resort $path failed: $err"; }
##############################################
libchado-perl-1.31/lib/Bio/GMOD/Bulkfiles.pm-2434-      open(SH,">$spath"); print SH $fixme->{content}; close(SH);
libchado-perl-1.31/lib/Bio/GMOD/Bulkfiles.pm:2435:      my $sresult= `$shell $spath $fixinput`; #?? what of perl params 
libchado-perl-1.31/lib/Bio/GMOD/Bulkfiles.pm-2436-      # how do i pipe table into script ?? and out again to replace old
##############################################
libchado-perl-1.31/lib/Bio/GMOD/Bulkfiles.pm-2838-      else { $oroot= "./"; }  
libchado-perl-1.31/lib/Bio/GMOD/Bulkfiles.pm:2839:      $oroot=`cd "$oroot" && pwd`; chomp($oroot);
libchado-perl-1.31/lib/Bio/GMOD/Bulkfiles.pm-2840-      }
##############################################
libchado-perl-1.31/lib/Bio/GMOD/Bulkfiles/BulkWriter.pm-545-    my $topath  = catfile($todir, $toname);
libchado-perl-1.31/lib/Bio/GMOD/Bulkfiles/BulkWriter.pm:546:    system('/bin/cp', '-p', $frompath, $topath);
libchado-perl-1.31/lib/Bio/GMOD/Bulkfiles/BulkWriter.pm-547-    print STDERR "copy $frompath to $toname\n" if $DEBUG; 
##############################################
libchado-perl-1.31/lib/Bio/GMOD/Bulkfiles/FeatureWriter.pm-501-    my $to  = $mapname_pattern{$mp}->{to};
libchado-perl-1.31/lib/Bio/GMOD/Bulkfiles/FeatureWriter.pm:502:    if ($to =~ /\$/) { $name =~ s/$from/eval($to)/e; }
libchado-perl-1.31/lib/Bio/GMOD/Bulkfiles/FeatureWriter.pm-503-    else { $name =~ s/$from/$to/g; }
##############################################
libchado-perl-1.31/lib/Bio/GMOD/Bulkfiles/FeatureWriter.pm-920-    my $to  = $mapattr_pattern{$mp}->{to};
libchado-perl-1.31/lib/Bio/GMOD/Bulkfiles/FeatureWriter.pm:921:    if ($to =~ /\$/) { $attribute =~ s/$from/eval($to)/e; }
libchado-perl-1.31/lib/Bio/GMOD/Bulkfiles/FeatureWriter.pm-922-    else { $attribute =~ s/$from/$to/g; }
##############################################
libchado-perl-1.31/lib/Bio/GMOD/Bulkfiles/BlastWriter.pm-467-    
libchado-perl-1.31/lib/Bio/GMOD/Bulkfiles/BlastWriter.pm:468:  system("$cat $seqlib | $formatdb $opts -i stdin ");
libchado-perl-1.31/lib/Bio/GMOD/Bulkfiles/BlastWriter.pm-469-  opendir(D,"."); my @f= grep(/stdin/,readdir(D)); closedir(D);
##############################################
libchado-perl-1.31/lib/Bio/GMOD/Bulkfiles/BlastWriter.pm-492-  warn("$cat $seqlib | $formatdb $opts -i stdin \n") if $DEBUG;
libchado-perl-1.31/lib/Bio/GMOD/Bulkfiles/BlastWriter.pm:493:  system("$cat $seqlib | $formatdb $opts -i stdin ");
libchado-perl-1.31/lib/Bio/GMOD/Bulkfiles/BlastWriter.pm-494-  
##############################################
libchado-perl-1.31/lib/Bio/GMOD/Bulkfiles/GenbankSubmitWriter.pm-235-
libchado-perl-1.31/lib/Bio/GMOD/Bulkfiles/GenbankSubmitWriter.pm:236:  my $ok= system("$tbl2asn $opts ");
libchado-perl-1.31/lib/Bio/GMOD/Bulkfiles/GenbankSubmitWriter.pm-237-  
##############################################
libchado-perl-1.31/lib/Bio/GMOD/Bulkfiles/GenbankSubmitWriter.pm-489-#     my $to  = $mapname_pattern{$mp}->{to};
libchado-perl-1.31/lib/Bio/GMOD/Bulkfiles/GenbankSubmitWriter.pm:490:#     if ($to =~ /\$/) { $name =~ s/$from/eval($to)/e; }
libchado-perl-1.31/lib/Bio/GMOD/Bulkfiles/GenbankSubmitWriter.pm-491-#     else { $name =~ s/$from/$to/g; }
##############################################
libchado-perl-1.31/lib/Bio/GMOD/Bulkfiles/GenbankSubmitWriter.pm-667-    my $to  = $mapattr_pattern{$mp}->{to};
libchado-perl-1.31/lib/Bio/GMOD/Bulkfiles/GenbankSubmitWriter.pm:668:    if ($to =~ /\$/) { $attribute =~ s/$from/eval($to)/e; }
libchado-perl-1.31/lib/Bio/GMOD/Bulkfiles/GenbankSubmitWriter.pm-669-    else { $attribute =~ s/$from/$to/g; }
##############################################
libchado-perl-1.31/lib/Bio/GMOD/Load/GFF.pm-694-    warn "gfffile: $gfffile" if DEBUG;
libchado-perl-1.31/lib/Bio/GMOD/Load/GFF.pm:695:    my $linenumber = `grep -n "^>" $gfffile`;
libchado-perl-1.31/lib/Bio/GMOD/Load/GFF.pm-696-    if ( $linenumber =~ /^(\d+)/ ) {
libchado-perl-1.31/lib/Bio/GMOD/Load/GFF.pm-697-        $linenumber = $1;
libchado-perl-1.31/lib/Bio/GMOD/Load/GFF.pm:698:        system("tail +$linenumber $self->gfffile() > ".$self->tmpfasta() );
libchado-perl-1.31/lib/Bio/GMOD/Load/GFF.pm-699-        $linenumber -= 1;
libchado-perl-1.31/lib/Bio/GMOD/Load/GFF.pm:700:        system("head -$linenumber $self->gfffile() > ".$self->tmpgff() );
libchado-perl-1.31/lib/Bio/GMOD/Load/GFF.pm-701-
##############################################
libchado-perl-1.31/lib/Bio/GMOD/Config2.pm-568-    $dir= "$dir/.."; ##NOT File::Basename::dirname($dir)."/..";
libchado-perl-1.31/lib/Bio/GMOD/Config2.pm:569:    $dir=`cd "$dir" && pwd`; chomp($dir);
libchado-perl-1.31/lib/Bio/GMOD/Config2.pm-570-    ##warn " _updir $dir\n" if $DEBUG;
##############################################
libchado-perl-1.31/load/bin/load_gff3.PLS-840-      )
libchado-perl-1.31/load/bin/load_gff3.PLS:841:      or ( system( 'pod2text', $0 ), exit -1 );
libchado-perl-1.31/load/bin/load_gff3.PLS-842-
##############################################
libchado-perl-1.31/load/bin/load_gff3.PLS-870-
libchado-perl-1.31/load/bin/load_gff3.PLS:871:    my $linenumber = `grep -n "^>" $GFFFILE`;
libchado-perl-1.31/load/bin/load_gff3.PLS-872-    if ( $linenumber =~ /^(\d+)/ ) {
libchado-perl-1.31/load/bin/load_gff3.PLS-873-        $linenumber = $1;
libchado-perl-1.31/load/bin/load_gff3.PLS:874:        system("tail -n +$linenumber $GFFFILE > $TMPFASTA");
libchado-perl-1.31/load/bin/load_gff3.PLS-875-        $linenumber -= 1;
libchado-perl-1.31/load/bin/load_gff3.PLS:876:        system("head -n $linenumber $GFFFILE > $TMPGFF");
libchado-perl-1.31/load/bin/load_gff3.PLS-877-
##############################################
libchado-perl-1.31/load/bin/bulk_load_gff3.PLS-618-) 
libchado-perl-1.31/load/bin/bulk_load_gff3.PLS:619:# or ( system( 'pod2text', $0 ), exit -1 );
libchado-perl-1.31/load/bin/bulk_load_gff3.PLS-620-or pod2usage(-verbose => 1, -exitval => 1);
##############################################
libchado-perl-1.31/schemas/1-1.21/diff.sql-521- );
libchado-perl-1.31/schemas/1-1.21/diff.sql:522:COMMENT ON TABLE stock_relationship_cvterm is 'For germplasm maintenance and pedigree data, stock_relationship. type_id will record cvterms such as "is a female parent of", "a parent for mutation", "is a group_id of", "is a source_id of", etc The cvterms for higher categories such as "generative", "derivative" or "maintenance" can be stored in table stock_relationship_cvterm';
libchado-perl-1.31/schemas/1-1.21/diff.sql-523-
##############################################
libchado-perl-1.31/schemas/1.1-1.21/diff.sql-140- );
libchado-perl-1.31/schemas/1.1-1.21/diff.sql:141:COMMENT ON TABLE stock_relationship_cvterm is 'For germplasm maintenance and pedigree data, stock_relationship. type_id will record cvterms such as "is a female parent of", "a parent for mutation", "is a group_id of", "is a source_id of", etc The cvterms for higher categories such as "generative", "derivative" or "maintenance" can be stored in table stock_relationship_cvterm';
libchado-perl-1.31/schemas/1.1-1.21/diff.sql-142-
##############################################
libchado-perl-1.31/schemas/1.1-1.21/diff-94-> --- *** Any one of several small cytoplasmic RNA ***
libchado-perl-1.31/schemas/1.1-1.21/diff:95:> --- ***  molecules present in the cytoplasm and  ***
libchado-perl-1.31/schemas/1.1-1.21/diff-96-> --- *** sometimes nucleus of a eukaryote.        ***
##############################################
libchado-perl-1.31/schemas/1.1-1.21/diff-10653-< );
libchado-perl-1.31/schemas/1.1-1.21/diff:10654:< COMMENT ON TABLE stock_relationship_cvterm is 'For germplasm maintenance and pedigree data, stock_relationship. type_id will record cvterms such as "is a female parent of", "a parent for mutation", "is a group_id of", "is a source_id of", etc The cvterms for higher categories such as "generative", "derivative" or "maintenance" can be stored in table stock_relationship_cvterm';
libchado-perl-1.31/schemas/1.1-1.21/diff-10655-< 
##############################################
libchado-perl-1.31/schemas/1.1-1.21/diff-10805-> --FROM expression s, feature_expression fs
libchado-perl-1.31/schemas/1.1-1.21/diff:10806:> --WHERE fs.feature_id= $1 AND fs.expression_id = s.expression_id
libchado-perl-1.31/schemas/1.1-1.21/diff-10807-> --UNION
##############################################
libchado-perl-1.31/schemas/1.1-1.21/diff-10809-> --FROM gcontext g, feature_gcontext fg
libchado-perl-1.31/schemas/1.1-1.21/diff:10810:> --WHERE fg.feature_id= $1 AND g.gcontext_id = fg.gcontext_id
libchado-perl-1.31/schemas/1.1-1.21/diff-10811-> --UNION
##############################################
libchado-perl-1.31/schemas/1.1-1.21/diff-10813-> --FROM genotype s, feature_genotype fs
libchado-perl-1.31/schemas/1.1-1.21/diff:10814:> --WHERE fs.feature_id= $1 AND fs.genotype_id = s.genotype_id
libchado-perl-1.31/schemas/1.1-1.21/diff-10815-> --UNION
##############################################
libchado-perl-1.31/schemas/1.1-1.21/diff-10817-> --FROM phenotype s, feature_phenotype fs
libchado-perl-1.31/schemas/1.1-1.21/diff:10818:> --WHERE fs.feature_id= $1 AND fs.phenotype_id = s.phenotype_id
libchado-perl-1.31/schemas/1.1-1.21/diff-10819-41168c36443
##############################################
libchado-perl-1.31/schemas/1-1.11/diff-397-> --- *** eral small cytoplasmic RNA molecules pre ***
libchado-perl-1.31/schemas/1-1.11/diff:398:> --- *** sent in the cytoplasm and sometimes nucl ***
libchado-perl-1.31/schemas/1-1.11/diff-399-> --- *** eus of a eukaryote.                      ***
##############################################
libchado-perl-1.31/schemas/1-1.11/diff-415-> --- *** Any one of several small cytoplasmic RNA ***
libchado-perl-1.31/schemas/1-1.11/diff:416:> --- ***  molecules present in the cytoplasm and  ***
libchado-perl-1.31/schemas/1-1.11/diff-417-> --- *** sometimes nucleus of a eukaryote.        ***
##############################################
libchado-perl-1.31/schemas/1.23/default_schema.sql-1202-  FROM organism
libchado-perl-1.31/schemas/1.23/default_schema.sql:1203:  WHERE genus=$1
libchado-perl-1.31/schemas/1.23/default_schema.sql-1204-    AND species=$2
##############################################
libchado-perl-1.31/schemas/1.23/default_schema.sql-1210-  FROM organism
libchado-perl-1.31/schemas/1.23/default_schema.sql:1211:  WHERE genus=substring($1,1,position('' '' IN $1)-1)
libchado-perl-1.31/schemas/1.23/default_schema.sql-1212-    AND species=substring($1,position('' '' IN $1)+1)
##############################################
libchado-perl-1.31/schemas/1.23/default_schema.sql-1218-  FROM organism
libchado-perl-1.31/schemas/1.23/default_schema.sql:1219:  WHERE substr(genus,1,1)=substring($1,1,1)
libchado-perl-1.31/schemas/1.23/default_schema.sql-1220-    AND species=substring($1,position('' '' IN $1)+1)
##############################################
libchado-perl-1.31/schemas/1.23/default_schema.sql-2096-CREATE OR REPLACE FUNCTION translate_codon(TEXT,INT) RETURNS CHAR AS
libchado-perl-1.31/schemas/1.23/default_schema.sql:2097: 'SELECT aa FROM genetic_code.gencode_codon_aa WHERE codon=$1 AND gencode_id=$2'
libchado-perl-1.31/schemas/1.23/default_schema.sql-2098-LANGUAGE 'sql';
##############################################
libchado-perl-1.31/schemas/1.23/default_schema.sql-2412-  FROM cv INNER JOIN cvterm USING (cv_id)
libchado-perl-1.31/schemas/1.23/default_schema.sql:2413:  WHERE cvterm.name=$1 AND cv.name=''sequence''
libchado-perl-1.31/schemas/1.23/default_schema.sql-2414- ' LANGUAGE 'sql';
##############################################
libchado-perl-1.31/schemas/1.23/default_schema.sql-2419-  FROM cv INNER JOIN cvterm USING (cv_id)
libchado-perl-1.31/schemas/1.23/default_schema.sql:2420:  WHERE cvterm.name=$1 AND cv.name=''feature_property''
libchado-perl-1.31/schemas/1.23/default_schema.sql-2421- ' LANGUAGE 'sql';
##############################################
libchado-perl-1.31/schemas/1.23/default_schema.sql-2426-  FROM cv INNER JOIN cvterm USING (cv_id)
libchado-perl-1.31/schemas/1.23/default_schema.sql:2427:  WHERE cvterm.name=$1 AND cv.name=''relationship''
libchado-perl-1.31/schemas/1.23/default_schema.sql-2428- ' LANGUAGE 'sql';
##############################################
libchado-perl-1.31/schemas/1.23/default_schema.sql-2434-  FROM feature
libchado-perl-1.31/schemas/1.23/default_schema.sql:2435:  WHERE uniquename=$1
libchado-perl-1.31/schemas/1.23/default_schema.sql-2436-    AND type_id=get_feature_type_id($2)
##############################################
libchado-perl-1.31/schemas/1.23/default_schema.sql-2607---- *** eral small cytoplasmic RNA molecules pre ***
libchado-perl-1.31/schemas/1.23/default_schema.sql:2608:--- *** sent in the cytoplasm and sometimes nucl ***
libchado-perl-1.31/schemas/1.23/default_schema.sql-2609---- *** eus of a eukaryote.                      ***
##############################################
libchado-perl-1.31/schemas/1.23/default_schema.sql-37499-    AND g1.group_id = g2.group_id
libchado-perl-1.31/schemas/1.23/default_schema.sql:37500:    AND g1.srcfeature_id = (SELECT feature_id FROM feature WHERE uniquename = $3)
libchado-perl-1.31/schemas/1.23/default_schema.sql-37501-    AND boxquery($1, $2) @ boxrange(g1.fmin,g2.fmax)
##############################################
libchado-perl-1.31/schemas/1.23/default_schema.sql-37506-  FROM groupoverlaps($1,$2,$3)
libchado-perl-1.31/schemas/1.23/default_schema.sql:37507:  WHERE fmin <= $1 AND fmax >= $2
libchado-perl-1.31/schemas/1.23/default_schema.sql-37508-' LANGUAGE 'sql';
##############################################
libchado-perl-1.31/schemas/1.23/default_schema.sql-37512-  FROM groupoverlaps($1,$2,$3)
libchado-perl-1.31/schemas/1.23/default_schema.sql:37513:  WHERE fmin >= $1 AND fmax <= $2
libchado-perl-1.31/schemas/1.23/default_schema.sql-37514-' LANGUAGE 'sql';
##############################################
libchado-perl-1.31/schemas/1.23/default_schema.sql-37518-  FROM groupoverlaps($1,$2,$3)
libchado-perl-1.31/schemas/1.23/default_schema.sql:37519:  WHERE fmin = $1 AND fmax = $2
libchado-perl-1.31/schemas/1.23/default_schema.sql-37520-' LANGUAGE 'sql';
##############################################
libchado-perl-1.31/schemas/1.23/default_schema.sql-39100-    FROM phylonode
libchado-perl-1.31/schemas/1.23/default_schema.sql:39101:    WHERE parent_phylonode_id = $1
libchado-perl-1.31/schemas/1.23/default_schema.sql-39102-'
##############################################
libchado-perl-1.31/schemas/1.23/default_schema.sql-40411-);
libchado-perl-1.31/schemas/1.23/default_schema.sql:40412:COMMENT ON TABLE stock_relationship_cvterm is 'For germplasm maintenance and pedigree data, stock_relationship. type_id will record cvterms such as "is a female parent of", "a parent for mutation", "is a group_id of", "is a source_id of", etc The cvterms for higher categories such as "generative", "derivative" or "maintenance" can be stored in table stock_relationship_cvterm';
libchado-perl-1.31/schemas/1.23/default_schema.sql-40413-
##############################################
libchado-perl-1.31/schemas/1.23/default_schema.sql-41161-FROM cvterm s, feature_cvterm fs
libchado-perl-1.31/schemas/1.23/default_schema.sql:41162:WHERE fs.feature_id= $1 AND fs.cvterm_id = s.cvterm_id
libchado-perl-1.31/schemas/1.23/default_schema.sql-41163-UNION
##############################################
libchado-perl-1.31/schemas/1.23/default_schema.sql-41165-FROM dbxref s, feature_dbxref fs, db d
libchado-perl-1.31/schemas/1.23/default_schema.sql:41166:WHERE fs.feature_id= $1 AND fs.dbxref_id = s.dbxref_id AND s.db_id = d.db_id
libchado-perl-1.31/schemas/1.23/default_schema.sql-41167-UNION
##############################################
libchado-perl-1.31/schemas/1.23/default_schema.sql-41169-FROM synonym s, feature_synonym fs
libchado-perl-1.31/schemas/1.23/default_schema.sql:41170:WHERE fs.feature_id= $1 AND fs.synonym_id = s.synonym_id
libchado-perl-1.31/schemas/1.23/default_schema.sql-41171-UNION
##############################################
libchado-perl-1.31/schemas/1.23/default_schema.sql-41173-FROM featureprop fp, cvterm cv
libchado-perl-1.31/schemas/1.23/default_schema.sql:41174:WHERE fp.feature_id= $1 AND fp.type_id = cv.cvterm_id 
libchado-perl-1.31/schemas/1.23/default_schema.sql-41175-UNION
##############################################
libchado-perl-1.31/schemas/1.23/default_schema.sql-41177-FROM pub s, feature_pub fs
libchado-perl-1.31/schemas/1.23/default_schema.sql:41178:WHERE fs.feature_id= $1 AND fs.pub_id = s.pub_id
libchado-perl-1.31/schemas/1.23/default_schema.sql-41179-'
##############################################
libchado-perl-1.31/schemas/1.22/default_schema.sql-1202-  FROM organism
libchado-perl-1.31/schemas/1.22/default_schema.sql:1203:  WHERE genus=$1
libchado-perl-1.31/schemas/1.22/default_schema.sql-1204-    AND species=$2
##############################################
libchado-perl-1.31/schemas/1.22/default_schema.sql-1210-  FROM organism
libchado-perl-1.31/schemas/1.22/default_schema.sql:1211:  WHERE genus=substring($1,1,position('' '' IN $1)-1)
libchado-perl-1.31/schemas/1.22/default_schema.sql-1212-    AND species=substring($1,position('' '' IN $1)+1)
##############################################
libchado-perl-1.31/schemas/1.22/default_schema.sql-1218-  FROM organism
libchado-perl-1.31/schemas/1.22/default_schema.sql:1219:  WHERE substr(genus,1,1)=substring($1,1,1)
libchado-perl-1.31/schemas/1.22/default_schema.sql-1220-    AND species=substring($1,position('' '' IN $1)+1)
##############################################
libchado-perl-1.31/schemas/1.22/default_schema.sql-2096-CREATE OR REPLACE FUNCTION translate_codon(TEXT,INT) RETURNS CHAR AS
libchado-perl-1.31/schemas/1.22/default_schema.sql:2097: 'SELECT aa FROM genetic_code.gencode_codon_aa WHERE codon=$1 AND gencode_id=$2'
libchado-perl-1.31/schemas/1.22/default_schema.sql-2098-LANGUAGE 'sql';
##############################################
libchado-perl-1.31/schemas/1.22/default_schema.sql-2412-  FROM cv INNER JOIN cvterm USING (cv_id)
libchado-perl-1.31/schemas/1.22/default_schema.sql:2413:  WHERE cvterm.name=$1 AND cv.name=''sequence''
libchado-perl-1.31/schemas/1.22/default_schema.sql-2414- ' LANGUAGE 'sql';
##############################################
libchado-perl-1.31/schemas/1.22/default_schema.sql-2419-  FROM cv INNER JOIN cvterm USING (cv_id)
libchado-perl-1.31/schemas/1.22/default_schema.sql:2420:  WHERE cvterm.name=$1 AND cv.name=''feature_property''
libchado-perl-1.31/schemas/1.22/default_schema.sql-2421- ' LANGUAGE 'sql';
##############################################
libchado-perl-1.31/schemas/1.22/default_schema.sql-2426-  FROM cv INNER JOIN cvterm USING (cv_id)
libchado-perl-1.31/schemas/1.22/default_schema.sql:2427:  WHERE cvterm.name=$1 AND cv.name=''relationship''
libchado-perl-1.31/schemas/1.22/default_schema.sql-2428- ' LANGUAGE 'sql';
##############################################
libchado-perl-1.31/schemas/1.22/default_schema.sql-2434-  FROM feature
libchado-perl-1.31/schemas/1.22/default_schema.sql:2435:  WHERE uniquename=$1
libchado-perl-1.31/schemas/1.22/default_schema.sql-2436-    AND type_id=get_feature_type_id($2)
##############################################
libchado-perl-1.31/schemas/1.22/default_schema.sql-2607---- *** eral small cytoplasmic RNA molecules pre ***
libchado-perl-1.31/schemas/1.22/default_schema.sql:2608:--- *** sent in the cytoplasm and sometimes nucl ***
libchado-perl-1.31/schemas/1.22/default_schema.sql-2609---- *** eus of a eukaryote.                      ***
##############################################
libchado-perl-1.31/schemas/1.22/default_schema.sql-37499-    AND g1.group_id = g2.group_id
libchado-perl-1.31/schemas/1.22/default_schema.sql:37500:    AND g1.srcfeature_id = (SELECT feature_id FROM feature WHERE uniquename = $3)
libchado-perl-1.31/schemas/1.22/default_schema.sql-37501-    AND boxquery($1, $2) @ boxrange(g1.fmin,g2.fmax)
##############################################
libchado-perl-1.31/schemas/1.22/default_schema.sql-37506-  FROM groupoverlaps($1,$2,$3)
libchado-perl-1.31/schemas/1.22/default_schema.sql:37507:  WHERE fmin <= $1 AND fmax >= $2
libchado-perl-1.31/schemas/1.22/default_schema.sql-37508-' LANGUAGE 'sql';
##############################################
libchado-perl-1.31/schemas/1.22/default_schema.sql-37512-  FROM groupoverlaps($1,$2,$3)
libchado-perl-1.31/schemas/1.22/default_schema.sql:37513:  WHERE fmin >= $1 AND fmax <= $2
libchado-perl-1.31/schemas/1.22/default_schema.sql-37514-' LANGUAGE 'sql';
##############################################
libchado-perl-1.31/schemas/1.22/default_schema.sql-37518-  FROM groupoverlaps($1,$2,$3)
libchado-perl-1.31/schemas/1.22/default_schema.sql:37519:  WHERE fmin = $1 AND fmax = $2
libchado-perl-1.31/schemas/1.22/default_schema.sql-37520-' LANGUAGE 'sql';
##############################################
libchado-perl-1.31/schemas/1.22/default_schema.sql-39100-    FROM phylonode
libchado-perl-1.31/schemas/1.22/default_schema.sql:39101:    WHERE parent_phylonode_id = $1
libchado-perl-1.31/schemas/1.22/default_schema.sql-39102-'
##############################################
libchado-perl-1.31/schemas/1.22/default_schema.sql-40411-);
libchado-perl-1.31/schemas/1.22/default_schema.sql:40412:COMMENT ON TABLE stock_relationship_cvterm is 'For germplasm maintenance and pedigree data, stock_relationship. type_id will record cvterms such as "is a female parent of", "a parent for mutation", "is a group_id of", "is a source_id of", etc The cvterms for higher categories such as "generative", "derivative" or "maintenance" can be stored in table stock_relationship_cvterm';
libchado-perl-1.31/schemas/1.22/default_schema.sql-40413-
##############################################
libchado-perl-1.31/schemas/1.22/default_schema.sql-41161-FROM cvterm s, feature_cvterm fs
libchado-perl-1.31/schemas/1.22/default_schema.sql:41162:WHERE fs.feature_id= $1 AND fs.cvterm_id = s.cvterm_id
libchado-perl-1.31/schemas/1.22/default_schema.sql-41163-UNION
##############################################
libchado-perl-1.31/schemas/1.22/default_schema.sql-41165-FROM dbxref s, feature_dbxref fs, db d
libchado-perl-1.31/schemas/1.22/default_schema.sql:41166:WHERE fs.feature_id= $1 AND fs.dbxref_id = s.dbxref_id AND s.db_id = d.db_id
libchado-perl-1.31/schemas/1.22/default_schema.sql-41167-UNION
##############################################
libchado-perl-1.31/schemas/1.22/default_schema.sql-41169-FROM synonym s, feature_synonym fs
libchado-perl-1.31/schemas/1.22/default_schema.sql:41170:WHERE fs.feature_id= $1 AND fs.synonym_id = s.synonym_id
libchado-perl-1.31/schemas/1.22/default_schema.sql-41171-UNION
##############################################
libchado-perl-1.31/schemas/1.22/default_schema.sql-41173-FROM featureprop fp, cvterm cv
libchado-perl-1.31/schemas/1.22/default_schema.sql:41174:WHERE fp.feature_id= $1 AND fp.type_id = cv.cvterm_id 
libchado-perl-1.31/schemas/1.22/default_schema.sql-41175-UNION
##############################################
libchado-perl-1.31/schemas/1.22/default_schema.sql-41177-FROM pub s, feature_pub fs
libchado-perl-1.31/schemas/1.22/default_schema.sql:41178:WHERE fs.feature_id= $1 AND fs.pub_id = s.pub_id
libchado-perl-1.31/schemas/1.22/default_schema.sql-41179-'
##############################################
libchado-perl-1.31/schemas/1.21/default_schema.sql-1202-  FROM organism
libchado-perl-1.31/schemas/1.21/default_schema.sql:1203:  WHERE genus=$1
libchado-perl-1.31/schemas/1.21/default_schema.sql-1204-    AND species=$2
##############################################
libchado-perl-1.31/schemas/1.21/default_schema.sql-1210-  FROM organism
libchado-perl-1.31/schemas/1.21/default_schema.sql:1211:  WHERE genus=substring($1,1,position('' '' IN $1)-1)
libchado-perl-1.31/schemas/1.21/default_schema.sql-1212-    AND species=substring($1,position('' '' IN $1)+1)
##############################################
libchado-perl-1.31/schemas/1.21/default_schema.sql-1218-  FROM organism
libchado-perl-1.31/schemas/1.21/default_schema.sql:1219:  WHERE substr(genus,1,1)=substring($1,1,1)
libchado-perl-1.31/schemas/1.21/default_schema.sql-1220-    AND species=substring($1,position('' '' IN $1)+1)
##############################################
libchado-perl-1.31/schemas/1.21/default_schema.sql-2096-CREATE OR REPLACE FUNCTION translate_codon(TEXT,INT) RETURNS CHAR AS
libchado-perl-1.31/schemas/1.21/default_schema.sql:2097: 'SELECT aa FROM genetic_code.gencode_codon_aa WHERE codon=$1 AND gencode_id=$2'
libchado-perl-1.31/schemas/1.21/default_schema.sql-2098-LANGUAGE 'sql';
##############################################
libchado-perl-1.31/schemas/1.21/default_schema.sql-2412-  FROM cv INNER JOIN cvterm USING (cv_id)
libchado-perl-1.31/schemas/1.21/default_schema.sql:2413:  WHERE cvterm.name=$1 AND cv.name=''sequence''
libchado-perl-1.31/schemas/1.21/default_schema.sql-2414- ' LANGUAGE 'sql';
##############################################
libchado-perl-1.31/schemas/1.21/default_schema.sql-2419-  FROM cv INNER JOIN cvterm USING (cv_id)
libchado-perl-1.31/schemas/1.21/default_schema.sql:2420:  WHERE cvterm.name=$1 AND cv.name=''feature_property''
libchado-perl-1.31/schemas/1.21/default_schema.sql-2421- ' LANGUAGE 'sql';
##############################################
libchado-perl-1.31/schemas/1.21/default_schema.sql-2426-  FROM cv INNER JOIN cvterm USING (cv_id)
libchado-perl-1.31/schemas/1.21/default_schema.sql:2427:  WHERE cvterm.name=$1 AND cv.name=''relationship''
libchado-perl-1.31/schemas/1.21/default_schema.sql-2428- ' LANGUAGE 'sql';
##############################################
libchado-perl-1.31/schemas/1.21/default_schema.sql-2434-  FROM feature
libchado-perl-1.31/schemas/1.21/default_schema.sql:2435:  WHERE uniquename=$1
libchado-perl-1.31/schemas/1.21/default_schema.sql-2436-    AND type_id=get_feature_type_id($2)
##############################################
libchado-perl-1.31/schemas/1.21/default_schema.sql-2607---- *** eral small cytoplasmic RNA molecules pre ***
libchado-perl-1.31/schemas/1.21/default_schema.sql:2608:--- *** sent in the cytoplasm and sometimes nucl ***
libchado-perl-1.31/schemas/1.21/default_schema.sql-2609---- *** eus of a eukaryote.                      ***
##############################################
libchado-perl-1.31/schemas/1.21/default_schema.sql-37499-    AND g1.group_id = g2.group_id
libchado-perl-1.31/schemas/1.21/default_schema.sql:37500:    AND g1.srcfeature_id = (SELECT feature_id FROM feature WHERE uniquename = $3)
libchado-perl-1.31/schemas/1.21/default_schema.sql-37501-    AND boxquery($1, $2) @ boxrange(g1.fmin,g2.fmax)
##############################################
libchado-perl-1.31/schemas/1.21/default_schema.sql-37506-  FROM groupoverlaps($1,$2,$3)
libchado-perl-1.31/schemas/1.21/default_schema.sql:37507:  WHERE fmin <= $1 AND fmax >= $2
libchado-perl-1.31/schemas/1.21/default_schema.sql-37508-' LANGUAGE 'sql';
##############################################
libchado-perl-1.31/schemas/1.21/default_schema.sql-37512-  FROM groupoverlaps($1,$2,$3)
libchado-perl-1.31/schemas/1.21/default_schema.sql:37513:  WHERE fmin >= $1 AND fmax <= $2
libchado-perl-1.31/schemas/1.21/default_schema.sql-37514-' LANGUAGE 'sql';
##############################################
libchado-perl-1.31/schemas/1.21/default_schema.sql-37518-  FROM groupoverlaps($1,$2,$3)
libchado-perl-1.31/schemas/1.21/default_schema.sql:37519:  WHERE fmin = $1 AND fmax = $2
libchado-perl-1.31/schemas/1.21/default_schema.sql-37520-' LANGUAGE 'sql';
##############################################
libchado-perl-1.31/schemas/1.21/default_schema.sql-39100-    FROM phylonode
libchado-perl-1.31/schemas/1.21/default_schema.sql:39101:    WHERE parent_phylonode_id = $1
libchado-perl-1.31/schemas/1.21/default_schema.sql-39102-'
##############################################
libchado-perl-1.31/schemas/1.21/default_schema.sql-40411-);
libchado-perl-1.31/schemas/1.21/default_schema.sql:40412:COMMENT ON TABLE stock_relationship_cvterm is 'For germplasm maintenance and pedigree data, stock_relationship. type_id will record cvterms such as "is a female parent of", "a parent for mutation", "is a group_id of", "is a source_id of", etc The cvterms for higher categories such as "generative", "derivative" or "maintenance" can be stored in table stock_relationship_cvterm';
libchado-perl-1.31/schemas/1.21/default_schema.sql-40413-
##############################################
libchado-perl-1.31/schemas/1.21/default_schema.sql-41161-FROM cvterm s, feature_cvterm fs
libchado-perl-1.31/schemas/1.21/default_schema.sql:41162:WHERE fs.feature_id= $1 AND fs.cvterm_id = s.cvterm_id
libchado-perl-1.31/schemas/1.21/default_schema.sql-41163-UNION
##############################################
libchado-perl-1.31/schemas/1.21/default_schema.sql-41165-FROM dbxref s, feature_dbxref fs, db d
libchado-perl-1.31/schemas/1.21/default_schema.sql:41166:WHERE fs.feature_id= $1 AND fs.dbxref_id = s.dbxref_id AND s.db_id = d.db_id
libchado-perl-1.31/schemas/1.21/default_schema.sql-41167-UNION
##############################################
libchado-perl-1.31/schemas/1.21/default_schema.sql-41169-FROM synonym s, feature_synonym fs
libchado-perl-1.31/schemas/1.21/default_schema.sql:41170:WHERE fs.feature_id= $1 AND fs.synonym_id = s.synonym_id
libchado-perl-1.31/schemas/1.21/default_schema.sql-41171-UNION
##############################################
libchado-perl-1.31/schemas/1.21/default_schema.sql-41173-FROM featureprop fp, cvterm cv
libchado-perl-1.31/schemas/1.21/default_schema.sql:41174:WHERE fp.feature_id= $1 AND fp.type_id = cv.cvterm_id 
libchado-perl-1.31/schemas/1.21/default_schema.sql-41175-UNION
##############################################
libchado-perl-1.31/schemas/1.21/default_schema.sql-41177-FROM pub s, feature_pub fs
libchado-perl-1.31/schemas/1.21/default_schema.sql:41178:WHERE fs.feature_id= $1 AND fs.pub_id = s.pub_id
libchado-perl-1.31/schemas/1.21/default_schema.sql-41179-'
##############################################
libchado-perl-1.31/schemas/1-1.1/diff-397-> --- *** eral small cytoplasmic RNA molecules pre ***
libchado-perl-1.31/schemas/1-1.1/diff:398:> --- *** sent in the cytoplasm and sometimes nucl ***
libchado-perl-1.31/schemas/1-1.1/diff-399-> --- *** eus of a eukaryote.                      ***
##############################################
libchado-perl-1.31/schemas/1-1.1/diff-415-> --- *** Any one of several small cytoplasmic RNA ***
libchado-perl-1.31/schemas/1-1.1/diff:416:> --- ***  molecules present in the cytoplasm and  ***
libchado-perl-1.31/schemas/1-1.1/diff-417-> --- *** sometimes nucleus of a eukaryote.        ***
##############################################
libchado-perl-1.31/schemas/1.1-1.2/diff.sql-140- );
libchado-perl-1.31/schemas/1.1-1.2/diff.sql:141:COMMENT ON TABLE stock_relationship_cvterm is 'For germplasm maintenance and pedigree data, stock_relationship. type_id will record cvterms such as "is a female parent of", "a parent for mutation", "is a group_id of", "is a source_id of", etc The cvterms for higher categories such as "generative", "derivative" or "maintenance" can be stored in table stock_relationship_cvterm';
libchado-perl-1.31/schemas/1.1-1.2/diff.sql-142-
##############################################
libchado-perl-1.31/schemas/1.1-1.2/diff-94-> --- *** Any one of several small cytoplasmic RNA ***
libchado-perl-1.31/schemas/1.1-1.2/diff:95:> --- ***  molecules present in the cytoplasm and  ***
libchado-perl-1.31/schemas/1.1-1.2/diff-96-> --- *** sometimes nucleus of a eukaryote.        ***
##############################################
libchado-perl-1.31/schemas/1.1-1.2/diff-10653-< );
libchado-perl-1.31/schemas/1.1-1.2/diff:10654:< COMMENT ON TABLE stock_relationship_cvterm is 'For germplasm maintenance and pedigree data, stock_relationship. type_id will record cvterms such as "is a female parent of", "a parent for mutation", "is a group_id of", "is a source_id of", etc The cvterms for higher categories such as "generative", "derivative" or "maintenance" can be stored in table stock_relationship_cvterm';
libchado-perl-1.31/schemas/1.1-1.2/diff-10655-< 
##############################################
libchado-perl-1.31/schemas/1.1-1.2/diff-10805-> --FROM expression s, feature_expression fs
libchado-perl-1.31/schemas/1.1-1.2/diff:10806:> --WHERE fs.feature_id= $1 AND fs.expression_id = s.expression_id
libchado-perl-1.31/schemas/1.1-1.2/diff-10807-> --UNION
##############################################
libchado-perl-1.31/schemas/1.1-1.2/diff-10809-> --FROM gcontext g, feature_gcontext fg
libchado-perl-1.31/schemas/1.1-1.2/diff:10810:> --WHERE fg.feature_id= $1 AND g.gcontext_id = fg.gcontext_id
libchado-perl-1.31/schemas/1.1-1.2/diff-10811-> --UNION
##############################################
libchado-perl-1.31/schemas/1.1-1.2/diff-10813-> --FROM genotype s, feature_genotype fs
libchado-perl-1.31/schemas/1.1-1.2/diff:10814:> --WHERE fs.feature_id= $1 AND fs.genotype_id = s.genotype_id
libchado-perl-1.31/schemas/1.1-1.2/diff-10815-> --UNION
##############################################
libchado-perl-1.31/schemas/1.1-1.2/diff-10817-> --FROM phenotype s, feature_phenotype fs
libchado-perl-1.31/schemas/1.1-1.2/diff:10818:> --WHERE fs.feature_id= $1 AND fs.phenotype_id = s.phenotype_id
libchado-perl-1.31/schemas/1.1-1.2/diff-10819-41168c36443
##############################################
libchado-perl-1.31/schemas/1/default_schema.sql-1165-  FROM organism
libchado-perl-1.31/schemas/1/default_schema.sql:1166:  WHERE genus=$1
libchado-perl-1.31/schemas/1/default_schema.sql-1167-    AND species=$2
##############################################
libchado-perl-1.31/schemas/1/default_schema.sql-1173-  FROM organism
libchado-perl-1.31/schemas/1/default_schema.sql:1174:  WHERE genus=substring($1,1,position('' '' IN $1)-1)
libchado-perl-1.31/schemas/1/default_schema.sql-1175-    AND species=substring($1,position('' '' IN $1)+1)
##############################################
libchado-perl-1.31/schemas/1/default_schema.sql-1181-  FROM organism
libchado-perl-1.31/schemas/1/default_schema.sql:1182:  WHERE substr(genus,1,1)=substring($1,1,1)
libchado-perl-1.31/schemas/1/default_schema.sql-1183-    AND species=substring($1,position('' '' IN $1)+1)
##############################################
libchado-perl-1.31/schemas/1/default_schema.sql-2053-CREATE OR REPLACE FUNCTION translate_codon(TEXT,INT) RETURNS CHAR AS
libchado-perl-1.31/schemas/1/default_schema.sql:2054: 'SELECT aa FROM genetic_code.gencode_codon_aa WHERE codon=$1 AND gencode_id=$2'
libchado-perl-1.31/schemas/1/default_schema.sql-2055-LANGUAGE 'sql';
##############################################
libchado-perl-1.31/schemas/1/default_schema.sql-2184-  FROM cv INNER JOIN cvterm USING (cv_id)
libchado-perl-1.31/schemas/1/default_schema.sql:2185:  WHERE cvterm.name=$1 AND cv.name=''sequence''
libchado-perl-1.31/schemas/1/default_schema.sql-2186- ' LANGUAGE 'sql';
##############################################
libchado-perl-1.31/schemas/1/default_schema.sql-2191-  FROM cv INNER JOIN cvterm USING (cv_id)
libchado-perl-1.31/schemas/1/default_schema.sql:2192:  WHERE cvterm.name=$1 AND cv.name=''feature_property''
libchado-perl-1.31/schemas/1/default_schema.sql-2193- ' LANGUAGE 'sql';
##############################################
libchado-perl-1.31/schemas/1/default_schema.sql-2198-  FROM cv INNER JOIN cvterm USING (cv_id)
libchado-perl-1.31/schemas/1/default_schema.sql:2199:  WHERE cvterm.name=$1 AND cv.name=''relationship''
libchado-perl-1.31/schemas/1/default_schema.sql-2200- ' LANGUAGE 'sql';
##############################################
libchado-perl-1.31/schemas/1/default_schema.sql-2206-  FROM feature
libchado-perl-1.31/schemas/1/default_schema.sql:2207:  WHERE uniquename=$1
libchado-perl-1.31/schemas/1/default_schema.sql-2208-    AND type_id=get_feature_type_id($2)
##############################################
libchado-perl-1.31/schemas/1/default_schema.sql-2683-    AND g1.group_id = g2.group_id
libchado-perl-1.31/schemas/1/default_schema.sql:2684:    AND g1.srcfeature_id = (SELECT feature_id FROM feature WHERE uniquename = $3)
libchado-perl-1.31/schemas/1/default_schema.sql-2685-    AND boxquery($1, $2) @ boxrange(g1.fmin,g2.fmax)
##############################################
libchado-perl-1.31/schemas/1/default_schema.sql-2690-  FROM groupoverlaps($1,$2,$3)
libchado-perl-1.31/schemas/1/default_schema.sql:2691:  WHERE fmin <= $1 AND fmax >= $2
libchado-perl-1.31/schemas/1/default_schema.sql-2692-' LANGUAGE 'sql';
##############################################
libchado-perl-1.31/schemas/1/default_schema.sql-2696-  FROM groupoverlaps($1,$2,$3)
libchado-perl-1.31/schemas/1/default_schema.sql:2697:  WHERE fmin >= $1 AND fmax <= $2
libchado-perl-1.31/schemas/1/default_schema.sql-2698-' LANGUAGE 'sql';
##############################################
libchado-perl-1.31/schemas/1/default_schema.sql-2702-  FROM groupoverlaps($1,$2,$3)
libchado-perl-1.31/schemas/1/default_schema.sql:2703:  WHERE fmin = $1 AND fmax = $2
libchado-perl-1.31/schemas/1/default_schema.sql-2704-' LANGUAGE 'sql';
##############################################
libchado-perl-1.31/schemas/1/default_schema.sql-4247-    FROM phylonode
libchado-perl-1.31/schemas/1/default_schema.sql:4248:    WHERE parent_phylonode_id = $1
libchado-perl-1.31/schemas/1/default_schema.sql-4249-'
##############################################
libchado-perl-1.31/schemas/1/default_schema.sql-5926-FROM cvterm s, feature_cvterm fs
libchado-perl-1.31/schemas/1/default_schema.sql:5927:WHERE fs.feature_id= $1 AND fs.cvterm_id = s.cvterm_id
libchado-perl-1.31/schemas/1/default_schema.sql-5928-UNION
##############################################
libchado-perl-1.31/schemas/1/default_schema.sql-5930-FROM dbxref s, feature_dbxref fs, db d
libchado-perl-1.31/schemas/1/default_schema.sql:5931:WHERE fs.feature_id= $1 AND fs.dbxref_id = s.dbxref_id AND s.db_id = d.db_id
libchado-perl-1.31/schemas/1/default_schema.sql-5932---UNION
##############################################
libchado-perl-1.31/schemas/1/default_schema.sql-5934---FROM expression s, feature_expression fs
libchado-perl-1.31/schemas/1/default_schema.sql:5935:--WHERE fs.feature_id= $1 AND fs.expression_id = s.expression_id
libchado-perl-1.31/schemas/1/default_schema.sql-5936---UNION
##############################################
libchado-perl-1.31/schemas/1/default_schema.sql-5938---FROM gcontext g, feature_gcontext fg
libchado-perl-1.31/schemas/1/default_schema.sql:5939:--WHERE fg.feature_id= $1 AND g.gcontext_id = fg.gcontext_id
libchado-perl-1.31/schemas/1/default_schema.sql-5940---UNION
##############################################
libchado-perl-1.31/schemas/1/default_schema.sql-5942---FROM genotype s, feature_genotype fs
libchado-perl-1.31/schemas/1/default_schema.sql:5943:--WHERE fs.feature_id= $1 AND fs.genotype_id = s.genotype_id
libchado-perl-1.31/schemas/1/default_schema.sql-5944---UNION
##############################################
libchado-perl-1.31/schemas/1/default_schema.sql-5946---FROM phenotype s, feature_phenotype fs
libchado-perl-1.31/schemas/1/default_schema.sql:5947:--WHERE fs.feature_id= $1 AND fs.phenotype_id = s.phenotype_id
libchado-perl-1.31/schemas/1/default_schema.sql-5948-UNION
##############################################
libchado-perl-1.31/schemas/1/default_schema.sql-5950-FROM synonym s, feature_synonym fs
libchado-perl-1.31/schemas/1/default_schema.sql:5951:WHERE fs.feature_id= $1 AND fs.synonym_id = s.synonym_id
libchado-perl-1.31/schemas/1/default_schema.sql-5952-UNION
##############################################
libchado-perl-1.31/schemas/1/default_schema.sql-5954-FROM featureprop fp, cvterm cv
libchado-perl-1.31/schemas/1/default_schema.sql:5955:WHERE fp.feature_id= $1 AND fp.type_id = cv.cvterm_id 
libchado-perl-1.31/schemas/1/default_schema.sql-5956-UNION
##############################################
libchado-perl-1.31/schemas/1/default_schema.sql-5958-FROM pub s, feature_pub fs
libchado-perl-1.31/schemas/1/default_schema.sql:5959:WHERE fs.feature_id= $1 AND fs.pub_id = s.pub_id
libchado-perl-1.31/schemas/1/default_schema.sql-5960-'
##############################################
libchado-perl-1.31/schemas/1.31/default_schema.sql-1467-  FROM organism
libchado-perl-1.31/schemas/1.31/default_schema.sql:1468:  WHERE genus=$1
libchado-perl-1.31/schemas/1.31/default_schema.sql-1469-    AND species=$2
##############################################
libchado-perl-1.31/schemas/1.31/default_schema.sql-1475-  FROM organism
libchado-perl-1.31/schemas/1.31/default_schema.sql:1476:  WHERE genus=substring($1,1,position('' '' IN $1)-1)
libchado-perl-1.31/schemas/1.31/default_schema.sql-1477-    AND species=substring($1,position('' '' IN $1)+1)
##############################################
libchado-perl-1.31/schemas/1.31/default_schema.sql-1483-  FROM organism
libchado-perl-1.31/schemas/1.31/default_schema.sql:1484:  WHERE substr(genus,1,1)=substring($1,1,1)
libchado-perl-1.31/schemas/1.31/default_schema.sql-1485-    AND species=substring($1,position('' '' IN $1)+1)
##############################################
libchado-perl-1.31/schemas/1.31/default_schema.sql-2385-CREATE OR REPLACE FUNCTION translate_codon(TEXT,BIGINT) RETURNS CHAR AS
libchado-perl-1.31/schemas/1.31/default_schema.sql:2386: 'SELECT aa FROM genetic_code.gencode_codon_aa WHERE codon=$1 AND gencode_id=$2'
libchado-perl-1.31/schemas/1.31/default_schema.sql-2387-LANGUAGE 'sql';
##############################################
libchado-perl-1.31/schemas/1.31/default_schema.sql-2701-  FROM cv INNER JOIN cvterm USING (cv_id)
libchado-perl-1.31/schemas/1.31/default_schema.sql:2702:  WHERE cvterm.name=$1 AND cv.name=''sequence''
libchado-perl-1.31/schemas/1.31/default_schema.sql-2703- ' LANGUAGE 'sql';
##############################################
libchado-perl-1.31/schemas/1.31/default_schema.sql-2708-  FROM cv INNER JOIN cvterm USING (cv_id)
libchado-perl-1.31/schemas/1.31/default_schema.sql:2709:  WHERE cvterm.name=$1 AND cv.name=''feature_property''
libchado-perl-1.31/schemas/1.31/default_schema.sql-2710- ' LANGUAGE 'sql';
##############################################
libchado-perl-1.31/schemas/1.31/default_schema.sql-2715-  FROM cv INNER JOIN cvterm USING (cv_id)
libchado-perl-1.31/schemas/1.31/default_schema.sql:2716:  WHERE cvterm.name=$1 AND cv.name=''relationship''
libchado-perl-1.31/schemas/1.31/default_schema.sql-2717- ' LANGUAGE 'sql';
##############################################
libchado-perl-1.31/schemas/1.31/default_schema.sql-2723-  FROM feature
libchado-perl-1.31/schemas/1.31/default_schema.sql:2724:  WHERE uniquename=$1
libchado-perl-1.31/schemas/1.31/default_schema.sql-2725-    AND type_id=get_feature_type_id($2)
##############################################
libchado-perl-1.31/schemas/1.31/default_schema.sql-2896---- *** eral small cytoplasmic RNA molecules pre ***
libchado-perl-1.31/schemas/1.31/default_schema.sql:2897:--- *** sent in the cytoplasm and sometimes nucl ***
libchado-perl-1.31/schemas/1.31/default_schema.sql-2898---- *** eus of a eukaryote.                      ***
##############################################
libchado-perl-1.31/schemas/1.31/default_schema.sql-37788-    AND g1.group_id = g2.group_id
libchado-perl-1.31/schemas/1.31/default_schema.sql:37789:    AND g1.srcfeature_id = (SELECT feature_id FROM feature WHERE uniquename = $3)
libchado-perl-1.31/schemas/1.31/default_schema.sql-37790-    AND boxquery($1, $2) @ boxrange(g1.fmin,g2.fmax)
##############################################
libchado-perl-1.31/schemas/1.31/default_schema.sql-37795-  FROM groupoverlaps($1,$2,$3)
libchado-perl-1.31/schemas/1.31/default_schema.sql:37796:  WHERE fmin <= $1 AND fmax >= $2
libchado-perl-1.31/schemas/1.31/default_schema.sql-37797-' LANGUAGE 'sql';
##############################################
libchado-perl-1.31/schemas/1.31/default_schema.sql-37801-  FROM groupoverlaps($1,$2,$3)
libchado-perl-1.31/schemas/1.31/default_schema.sql:37802:  WHERE fmin >= $1 AND fmax <= $2
libchado-perl-1.31/schemas/1.31/default_schema.sql-37803-' LANGUAGE 'sql';
##############################################
libchado-perl-1.31/schemas/1.31/default_schema.sql-37807-  FROM groupoverlaps($1,$2,$3)
libchado-perl-1.31/schemas/1.31/default_schema.sql:37808:  WHERE fmin = $1 AND fmax = $2
libchado-perl-1.31/schemas/1.31/default_schema.sql-37809-' LANGUAGE 'sql';
##############################################
libchado-perl-1.31/schemas/1.31/default_schema.sql-39668-    FROM phylonode
libchado-perl-1.31/schemas/1.31/default_schema.sql:39669:    WHERE parent_phylonode_id = $1
libchado-perl-1.31/schemas/1.31/default_schema.sql-39670-'
##############################################
libchado-perl-1.31/schemas/1.31/default_schema.sql-40337-);
libchado-perl-1.31/schemas/1.31/default_schema.sql:40338:COMMENT ON TABLE stock_relationship_cvterm is 'For germplasm maintenance and pedigree data, stock_relationship. type_id will record cvterms such as "is a female parent of", "a parent for mutation", "is a group_id of", "is a source_id of", etc The cvterms for higher categories such as "generative", "derivative" or "maintenance" can be stored in table stock_relationship_cvterm';
libchado-perl-1.31/schemas/1.31/default_schema.sql-40339-
##############################################
libchado-perl-1.31/schemas/1.31/default_schema.sql-42005-FROM cvterm s, feature_cvterm fs
libchado-perl-1.31/schemas/1.31/default_schema.sql:42006:WHERE fs.feature_id= $1 AND fs.cvterm_id = s.cvterm_id
libchado-perl-1.31/schemas/1.31/default_schema.sql-42007-UNION
##############################################
libchado-perl-1.31/schemas/1.31/default_schema.sql-42009-FROM dbxref s, feature_dbxref fs, db d
libchado-perl-1.31/schemas/1.31/default_schema.sql:42010:WHERE fs.feature_id= $1 AND fs.dbxref_id = s.dbxref_id AND s.db_id = d.db_id
libchado-perl-1.31/schemas/1.31/default_schema.sql-42011-UNION
##############################################
libchado-perl-1.31/schemas/1.31/default_schema.sql-42013-FROM synonym s, feature_synonym fs
libchado-perl-1.31/schemas/1.31/default_schema.sql:42014:WHERE fs.feature_id= $1 AND fs.synonym_id = s.synonym_id
libchado-perl-1.31/schemas/1.31/default_schema.sql-42015-UNION
##############################################
libchado-perl-1.31/schemas/1.31/default_schema.sql-42017-FROM featureprop fp, cvterm cv
libchado-perl-1.31/schemas/1.31/default_schema.sql:42018:WHERE fp.feature_id= $1 AND fp.type_id = cv.cvterm_id 
libchado-perl-1.31/schemas/1.31/default_schema.sql-42019-UNION
##############################################
libchado-perl-1.31/schemas/1.31/default_schema.sql-42021-FROM pub s, feature_pub fs
libchado-perl-1.31/schemas/1.31/default_schema.sql:42022:WHERE fs.feature_id= $1 AND fs.pub_id = s.pub_id
libchado-perl-1.31/schemas/1.31/default_schema.sql-42023-'
##############################################
libchado-perl-1.31/schemas/1.2/default_schema.sql-1202-  FROM organism
libchado-perl-1.31/schemas/1.2/default_schema.sql:1203:  WHERE genus=$1
libchado-perl-1.31/schemas/1.2/default_schema.sql-1204-    AND species=$2
##############################################
libchado-perl-1.31/schemas/1.2/default_schema.sql-1210-  FROM organism
libchado-perl-1.31/schemas/1.2/default_schema.sql:1211:  WHERE genus=substring($1,1,position('' '' IN $1)-1)
libchado-perl-1.31/schemas/1.2/default_schema.sql-1212-    AND species=substring($1,position('' '' IN $1)+1)
##############################################
libchado-perl-1.31/schemas/1.2/default_schema.sql-1218-  FROM organism
libchado-perl-1.31/schemas/1.2/default_schema.sql:1219:  WHERE substr(genus,1,1)=substring($1,1,1)
libchado-perl-1.31/schemas/1.2/default_schema.sql-1220-    AND species=substring($1,position('' '' IN $1)+1)
##############################################
libchado-perl-1.31/schemas/1.2/default_schema.sql-2096-CREATE OR REPLACE FUNCTION translate_codon(TEXT,INT) RETURNS CHAR AS
libchado-perl-1.31/schemas/1.2/default_schema.sql:2097: 'SELECT aa FROM genetic_code.gencode_codon_aa WHERE codon=$1 AND gencode_id=$2'
libchado-perl-1.31/schemas/1.2/default_schema.sql-2098-LANGUAGE 'sql';
##############################################
libchado-perl-1.31/schemas/1.2/default_schema.sql-2412-  FROM cv INNER JOIN cvterm USING (cv_id)
libchado-perl-1.31/schemas/1.2/default_schema.sql:2413:  WHERE cvterm.name=$1 AND cv.name=''sequence''
libchado-perl-1.31/schemas/1.2/default_schema.sql-2414- ' LANGUAGE 'sql';
##############################################
libchado-perl-1.31/schemas/1.2/default_schema.sql-2419-  FROM cv INNER JOIN cvterm USING (cv_id)
libchado-perl-1.31/schemas/1.2/default_schema.sql:2420:  WHERE cvterm.name=$1 AND cv.name=''feature_property''
libchado-perl-1.31/schemas/1.2/default_schema.sql-2421- ' LANGUAGE 'sql';
##############################################
libchado-perl-1.31/schemas/1.2/default_schema.sql-2426-  FROM cv INNER JOIN cvterm USING (cv_id)
libchado-perl-1.31/schemas/1.2/default_schema.sql:2427:  WHERE cvterm.name=$1 AND cv.name=''relationship''
libchado-perl-1.31/schemas/1.2/default_schema.sql-2428- ' LANGUAGE 'sql';
##############################################
libchado-perl-1.31/schemas/1.2/default_schema.sql-2434-  FROM feature
libchado-perl-1.31/schemas/1.2/default_schema.sql:2435:  WHERE uniquename=$1
libchado-perl-1.31/schemas/1.2/default_schema.sql-2436-    AND type_id=get_feature_type_id($2)
##############################################
libchado-perl-1.31/schemas/1.2/default_schema.sql-2607---- *** eral small cytoplasmic RNA molecules pre ***
libchado-perl-1.31/schemas/1.2/default_schema.sql:2608:--- *** sent in the cytoplasm and sometimes nucl ***
libchado-perl-1.31/schemas/1.2/default_schema.sql-2609---- *** eus of a eukaryote.                      ***
##############################################
libchado-perl-1.31/schemas/1.2/default_schema.sql-37499-    AND g1.group_id = g2.group_id
libchado-perl-1.31/schemas/1.2/default_schema.sql:37500:    AND g1.srcfeature_id = (SELECT feature_id FROM feature WHERE uniquename = $3)
libchado-perl-1.31/schemas/1.2/default_schema.sql-37501-    AND boxquery($1, $2) @ boxrange(g1.fmin,g2.fmax)
##############################################
libchado-perl-1.31/schemas/1.2/default_schema.sql-37506-  FROM groupoverlaps($1,$2,$3)
libchado-perl-1.31/schemas/1.2/default_schema.sql:37507:  WHERE fmin <= $1 AND fmax >= $2
libchado-perl-1.31/schemas/1.2/default_schema.sql-37508-' LANGUAGE 'sql';
##############################################
libchado-perl-1.31/schemas/1.2/default_schema.sql-37512-  FROM groupoverlaps($1,$2,$3)
libchado-perl-1.31/schemas/1.2/default_schema.sql:37513:  WHERE fmin >= $1 AND fmax <= $2
libchado-perl-1.31/schemas/1.2/default_schema.sql-37514-' LANGUAGE 'sql';
##############################################
libchado-perl-1.31/schemas/1.2/default_schema.sql-37518-  FROM groupoverlaps($1,$2,$3)
libchado-perl-1.31/schemas/1.2/default_schema.sql:37519:  WHERE fmin = $1 AND fmax = $2
libchado-perl-1.31/schemas/1.2/default_schema.sql-37520-' LANGUAGE 'sql';
##############################################
libchado-perl-1.31/schemas/1.2/default_schema.sql-39100-    FROM phylonode
libchado-perl-1.31/schemas/1.2/default_schema.sql:39101:    WHERE parent_phylonode_id = $1
libchado-perl-1.31/schemas/1.2/default_schema.sql-39102-'
##############################################
libchado-perl-1.31/schemas/1.2/default_schema.sql-40411-);
libchado-perl-1.31/schemas/1.2/default_schema.sql:40412:COMMENT ON TABLE stock_relationship_cvterm is 'For germplasm maintenance and pedigree data, stock_relationship. type_id will record cvterms such as "is a female parent of", "a parent for mutation", "is a group_id of", "is a source_id of", etc The cvterms for higher categories such as "generative", "derivative" or "maintenance" can be stored in table stock_relationship_cvterm';
libchado-perl-1.31/schemas/1.2/default_schema.sql-40413-
##############################################
libchado-perl-1.31/schemas/1.2/default_schema.sql-41161-FROM cvterm s, feature_cvterm fs
libchado-perl-1.31/schemas/1.2/default_schema.sql:41162:WHERE fs.feature_id= $1 AND fs.cvterm_id = s.cvterm_id
libchado-perl-1.31/schemas/1.2/default_schema.sql-41163-UNION
##############################################
libchado-perl-1.31/schemas/1.2/default_schema.sql-41165-FROM dbxref s, feature_dbxref fs, db d
libchado-perl-1.31/schemas/1.2/default_schema.sql:41166:WHERE fs.feature_id= $1 AND fs.dbxref_id = s.dbxref_id AND s.db_id = d.db_id
libchado-perl-1.31/schemas/1.2/default_schema.sql-41167-UNION
##############################################
libchado-perl-1.31/schemas/1.2/default_schema.sql-41169-FROM synonym s, feature_synonym fs
libchado-perl-1.31/schemas/1.2/default_schema.sql:41170:WHERE fs.feature_id= $1 AND fs.synonym_id = s.synonym_id
libchado-perl-1.31/schemas/1.2/default_schema.sql-41171-UNION
##############################################
libchado-perl-1.31/schemas/1.2/default_schema.sql-41173-FROM featureprop fp, cvterm cv
libchado-perl-1.31/schemas/1.2/default_schema.sql:41174:WHERE fp.feature_id= $1 AND fp.type_id = cv.cvterm_id 
libchado-perl-1.31/schemas/1.2/default_schema.sql-41175-UNION
##############################################
libchado-perl-1.31/schemas/1.2/default_schema.sql-41177-FROM pub s, feature_pub fs
libchado-perl-1.31/schemas/1.2/default_schema.sql:41178:WHERE fs.feature_id= $1 AND fs.pub_id = s.pub_id
libchado-perl-1.31/schemas/1.2/default_schema.sql-41179-'
##############################################
libchado-perl-1.31/schemas/1.11-1.2/diff.sql-140- );
libchado-perl-1.31/schemas/1.11-1.2/diff.sql:141:COMMENT ON TABLE stock_relationship_cvterm is 'For germplasm maintenance and pedigree data, stock_relationship. type_id will record cvterms such as "is a female parent of", "a parent for mutation", "is a group_id of", "is a source_id of", etc The cvterms for higher categories such as "generative", "derivative" or "maintenance" can be stored in table stock_relationship_cvterm';
libchado-perl-1.31/schemas/1.11-1.2/diff.sql-142-
##############################################
libchado-perl-1.31/schemas/1.11-1.2/diff-94-> --- *** Any one of several small cytoplasmic RNA ***
libchado-perl-1.31/schemas/1.11-1.2/diff:95:> --- ***  molecules present in the cytoplasm and  ***
libchado-perl-1.31/schemas/1.11-1.2/diff-96-> --- *** sometimes nucleus of a eukaryote.        ***
##############################################
libchado-perl-1.31/schemas/1.11-1.2/diff-10653-< );
libchado-perl-1.31/schemas/1.11-1.2/diff:10654:< COMMENT ON TABLE stock_relationship_cvterm is 'For germplasm maintenance and pedigree data, stock_relationship. type_id will record cvterms such as "is a female parent of", "a parent for mutation", "is a group_id of", "is a source_id of", etc The cvterms for higher categories such as "generative", "derivative" or "maintenance" can be stored in table stock_relationship_cvterm';
libchado-perl-1.31/schemas/1.11-1.2/diff-10655-< 
##############################################
libchado-perl-1.31/schemas/1.11-1.2/diff-10805-> --FROM expression s, feature_expression fs
libchado-perl-1.31/schemas/1.11-1.2/diff:10806:> --WHERE fs.feature_id= $1 AND fs.expression_id = s.expression_id
libchado-perl-1.31/schemas/1.11-1.2/diff-10807-> --UNION
##############################################
libchado-perl-1.31/schemas/1.11-1.2/diff-10809-> --FROM gcontext g, feature_gcontext fg
libchado-perl-1.31/schemas/1.11-1.2/diff:10810:> --WHERE fg.feature_id= $1 AND g.gcontext_id = fg.gcontext_id
libchado-perl-1.31/schemas/1.11-1.2/diff-10811-> --UNION
##############################################
libchado-perl-1.31/schemas/1.11-1.2/diff-10813-> --FROM genotype s, feature_genotype fs
libchado-perl-1.31/schemas/1.11-1.2/diff:10814:> --WHERE fs.feature_id= $1 AND fs.genotype_id = s.genotype_id
libchado-perl-1.31/schemas/1.11-1.2/diff-10815-> --UNION
##############################################
libchado-perl-1.31/schemas/1.11-1.2/diff-10817-> --FROM phenotype s, feature_phenotype fs
libchado-perl-1.31/schemas/1.11-1.2/diff:10818:> --WHERE fs.feature_id= $1 AND fs.phenotype_id = s.phenotype_id
libchado-perl-1.31/schemas/1.11-1.2/diff-10819-41168c36443
##############################################
libchado-perl-1.31/schemas/1.23-1.31/diff.sql-2109-    AND g1.group_id = g2.group_id
libchado-perl-1.31/schemas/1.23-1.31/diff.sql:2110:    AND g1.srcfeature_id = (SELECT feature_id FROM feature WHERE uniquename = $3)
libchado-perl-1.31/schemas/1.23-1.31/diff.sql-2111-    AND boxquery($1, $2) @ boxrange(g1.fmin,g2.fmax)
##############################################
libchado-perl-1.31/schemas/1.23-1.31/diff.sql-2160-  FROM groupoverlaps($1,$2,$3)
libchado-perl-1.31/schemas/1.23-1.31/diff.sql:2161:  WHERE fmin <= $1 AND fmax >= $2
libchado-perl-1.31/schemas/1.23-1.31/diff.sql-2162-$_$;
##############################################
libchado-perl-1.31/schemas/1.23-1.31/diff.sql-2210-  FROM groupoverlaps($1,$2,$3)
libchado-perl-1.31/schemas/1.23-1.31/diff.sql:2211:  WHERE fmin = $1 AND fmax = $2
libchado-perl-1.31/schemas/1.23-1.31/diff.sql-2212-$_$;
##############################################
libchado-perl-1.31/schemas/1.23-1.31/diff.sql-2260-  FROM groupoverlaps($1,$2,$3)
libchado-perl-1.31/schemas/1.23-1.31/diff.sql:2261:  WHERE fmin >= $1 AND fmax <= $2
libchado-perl-1.31/schemas/1.23-1.31/diff.sql-2262-$_$;
##############################################
libchado-perl-1.31/schemas/1.23-1.31/diff.sql-2483-    LANGUAGE sql
libchado-perl-1.31/schemas/1.23-1.31/diff.sql:2484:    AS $$SELECT cv_id FROM cv WHERE name='sequence'$$;
libchado-perl-1.31/schemas/1.23-1.31/diff.sql-2485-
##############################################
libchado-perl-1.31/schemas/1.23-1.31/diff.sql-2492-    LANGUAGE sql
libchado-perl-1.31/schemas/1.23-1.31/diff.sql:2493:    AS $$SELECT cv_id FROM cv WHERE name='relationship'$$;
libchado-perl-1.31/schemas/1.23-1.31/diff.sql-2494-
##############################################
libchado-perl-1.31/schemas/1.23-1.31/diff.sql-2500-    LANGUAGE sql
libchado-perl-1.31/schemas/1.23-1.31/diff.sql:2501:    AS $$SELECT cv_id FROM cv WHERE name='feature_property'$$;
libchado-perl-1.31/schemas/1.23-1.31/diff.sql-2502-
##############################################
libchado-perl-1.31/schemas/1.23-1.31/diff.sql-2585-  FROM feature
libchado-perl-1.31/schemas/1.23-1.31/diff.sql:2586:  WHERE uniquename=$1
libchado-perl-1.31/schemas/1.23-1.31/diff.sql-2587-    AND type_id=get_feature_type_id($2)
##############################################
libchado-perl-1.31/schemas/1.23-1.31/diff.sql-2599-  FROM cv INNER JOIN cvterm USING (cv_id)
libchado-perl-1.31/schemas/1.23-1.31/diff.sql:2600:  WHERE cvterm.name=$1 AND cv.name='relationship'
libchado-perl-1.31/schemas/1.23-1.31/diff.sql-2601- $_$;
##############################################
libchado-perl-1.31/schemas/1.23-1.31/diff.sql-2611-  FROM cv INNER JOIN cvterm USING (cv_id)
libchado-perl-1.31/schemas/1.23-1.31/diff.sql:2612:  WHERE cvterm.name=$1 AND cv.name='sequence'
libchado-perl-1.31/schemas/1.23-1.31/diff.sql-2613- $_$;
##############################################
libchado-perl-1.31/schemas/1.23-1.31/diff.sql-2623-  FROM cv INNER JOIN cvterm USING (cv_id)
libchado-perl-1.31/schemas/1.23-1.31/diff.sql:2624:  WHERE cvterm.name=$1 AND cv.name='feature_property'
libchado-perl-1.31/schemas/1.23-1.31/diff.sql-2625- $_$;
##############################################
libchado-perl-1.31/schemas/1.23-1.31/diff.sql-2636-  FROM organism
libchado-perl-1.31/schemas/1.23-1.31/diff.sql:2637:  WHERE genus=substring($1,1,position(' ' IN $1)-1)
libchado-perl-1.31/schemas/1.23-1.31/diff.sql-2638-    AND species=substring($1,position(' ' IN $1)+1)
##############################################
libchado-perl-1.31/schemas/1.23-1.31/diff.sql-2649-  FROM organism
libchado-perl-1.31/schemas/1.23-1.31/diff.sql:2650:  WHERE genus=$1
libchado-perl-1.31/schemas/1.23-1.31/diff.sql-2651-    AND species=$2
##############################################
libchado-perl-1.31/schemas/1.23-1.31/diff.sql-2662-  FROM organism
libchado-perl-1.31/schemas/1.23-1.31/diff.sql:2663:  WHERE substr(genus,1,1)=substring($1,1,1)
libchado-perl-1.31/schemas/1.23-1.31/diff.sql-2664-    AND species=substring($1,position(' ' IN $1)+1)
##############################################
libchado-perl-1.31/schemas/1.23-1.31/diff.sql-2778-    FROM phylonode
libchado-perl-1.31/schemas/1.23-1.31/diff.sql:2779:    WHERE parent_phylonode_id = $1
libchado-perl-1.31/schemas/1.23-1.31/diff.sql-2780-$_$;
##############################################
libchado-perl-1.31/schemas/1.23-1.31/diff.sql-53008-FROM cvterm s, feature_cvterm fs
libchado-perl-1.31/schemas/1.23-1.31/diff.sql:53009:WHERE fs.feature_id= $1 AND fs.cvterm_id = s.cvterm_id
libchado-perl-1.31/schemas/1.23-1.31/diff.sql-53010-UNION
##############################################
libchado-perl-1.31/schemas/1.23-1.31/diff.sql-53012-FROM dbxref s, feature_dbxref fs, db d
libchado-perl-1.31/schemas/1.23-1.31/diff.sql:53013:WHERE fs.feature_id= $1 AND fs.dbxref_id = s.dbxref_id AND s.db_id = d.db_id
libchado-perl-1.31/schemas/1.23-1.31/diff.sql-53014-UNION
##############################################
libchado-perl-1.31/schemas/1.23-1.31/diff.sql-53016-FROM synonym s, feature_synonym fs
libchado-perl-1.31/schemas/1.23-1.31/diff.sql:53017:WHERE fs.feature_id= $1 AND fs.synonym_id = s.synonym_id
libchado-perl-1.31/schemas/1.23-1.31/diff.sql-53018-UNION
##############################################
libchado-perl-1.31/schemas/1.23-1.31/diff.sql-53020-FROM featureprop fp, cvterm cv
libchado-perl-1.31/schemas/1.23-1.31/diff.sql:53021:WHERE fp.feature_id= $1 AND fp.type_id = cv.cvterm_id 
libchado-perl-1.31/schemas/1.23-1.31/diff.sql-53022-UNION
##############################################
libchado-perl-1.31/schemas/1.23-1.31/diff.sql-53024-FROM pub s, feature_pub fs
libchado-perl-1.31/schemas/1.23-1.31/diff.sql:53025:WHERE fs.feature_id= $1 AND fs.pub_id = s.pub_id
libchado-perl-1.31/schemas/1.23-1.31/diff.sql-53026-$_$;
##############################################
libchado-perl-1.31/schemas/1.11/default_schema.sql-1165-  FROM organism
libchado-perl-1.31/schemas/1.11/default_schema.sql:1166:  WHERE genus=$1
libchado-perl-1.31/schemas/1.11/default_schema.sql-1167-    AND species=$2
##############################################
libchado-perl-1.31/schemas/1.11/default_schema.sql-1173-  FROM organism
libchado-perl-1.31/schemas/1.11/default_schema.sql:1174:  WHERE genus=substring($1,1,position('' '' IN $1)-1)
libchado-perl-1.31/schemas/1.11/default_schema.sql-1175-    AND species=substring($1,position('' '' IN $1)+1)
##############################################
libchado-perl-1.31/schemas/1.11/default_schema.sql-1181-  FROM organism
libchado-perl-1.31/schemas/1.11/default_schema.sql:1182:  WHERE substr(genus,1,1)=substring($1,1,1)
libchado-perl-1.31/schemas/1.11/default_schema.sql-1183-    AND species=substring($1,position('' '' IN $1)+1)
##############################################
libchado-perl-1.31/schemas/1.11/default_schema.sql-2057-CREATE OR REPLACE FUNCTION translate_codon(TEXT,INT) RETURNS CHAR AS
libchado-perl-1.31/schemas/1.11/default_schema.sql:2058: 'SELECT aa FROM genetic_code.gencode_codon_aa WHERE codon=$1 AND gencode_id=$2'
libchado-perl-1.31/schemas/1.11/default_schema.sql-2059-LANGUAGE 'sql';
##############################################
libchado-perl-1.31/schemas/1.11/default_schema.sql-2373-  FROM cv INNER JOIN cvterm USING (cv_id)
libchado-perl-1.31/schemas/1.11/default_schema.sql:2374:  WHERE cvterm.name=$1 AND cv.name=''sequence''
libchado-perl-1.31/schemas/1.11/default_schema.sql-2375- ' LANGUAGE 'sql';
##############################################
libchado-perl-1.31/schemas/1.11/default_schema.sql-2380-  FROM cv INNER JOIN cvterm USING (cv_id)
libchado-perl-1.31/schemas/1.11/default_schema.sql:2381:  WHERE cvterm.name=$1 AND cv.name=''feature_property''
libchado-perl-1.31/schemas/1.11/default_schema.sql-2382- ' LANGUAGE 'sql';
##############################################
libchado-perl-1.31/schemas/1.11/default_schema.sql-2387-  FROM cv INNER JOIN cvterm USING (cv_id)
libchado-perl-1.31/schemas/1.11/default_schema.sql:2388:  WHERE cvterm.name=$1 AND cv.name=''relationship''
libchado-perl-1.31/schemas/1.11/default_schema.sql-2389- ' LANGUAGE 'sql';
##############################################
libchado-perl-1.31/schemas/1.11/default_schema.sql-2395-  FROM feature
libchado-perl-1.31/schemas/1.11/default_schema.sql:2396:  WHERE uniquename=$1
libchado-perl-1.31/schemas/1.11/default_schema.sql-2397-    AND type_id=get_feature_type_id($2)
##############################################
libchado-perl-1.31/schemas/1.11/default_schema.sql-2568---- *** eral small cytoplasmic RNA molecules pre ***
libchado-perl-1.31/schemas/1.11/default_schema.sql:2569:--- *** sent in the cytoplasm and sometimes nucl ***
libchado-perl-1.31/schemas/1.11/default_schema.sql-2570---- *** eus of a eukaryote.                      ***
##############################################
libchado-perl-1.31/schemas/1.11/default_schema.sql-2586---- *** Any one of several small cytoplasmic RNA ***
libchado-perl-1.31/schemas/1.11/default_schema.sql:2587:--- ***  molecules present in the cytoplasm and  ***
libchado-perl-1.31/schemas/1.11/default_schema.sql-2588---- *** sometimes nucleus of a eukaryote.        ***
##############################################
libchado-perl-1.31/schemas/1.11/default_schema.sql-32950-    AND g1.group_id = g2.group_id
libchado-perl-1.31/schemas/1.11/default_schema.sql:32951:    AND g1.srcfeature_id = (SELECT feature_id FROM feature WHERE uniquename = $3)
libchado-perl-1.31/schemas/1.11/default_schema.sql-32952-    AND boxquery($1, $2) @ boxrange(g1.fmin,g2.fmax)
##############################################
libchado-perl-1.31/schemas/1.11/default_schema.sql-32957-  FROM groupoverlaps($1,$2,$3)
libchado-perl-1.31/schemas/1.11/default_schema.sql:32958:  WHERE fmin <= $1 AND fmax >= $2
libchado-perl-1.31/schemas/1.11/default_schema.sql-32959-' LANGUAGE 'sql';
##############################################
libchado-perl-1.31/schemas/1.11/default_schema.sql-32963-  FROM groupoverlaps($1,$2,$3)
libchado-perl-1.31/schemas/1.11/default_schema.sql:32964:  WHERE fmin >= $1 AND fmax <= $2
libchado-perl-1.31/schemas/1.11/default_schema.sql-32965-' LANGUAGE 'sql';
##############################################
libchado-perl-1.31/schemas/1.11/default_schema.sql-32969-  FROM groupoverlaps($1,$2,$3)
libchado-perl-1.31/schemas/1.11/default_schema.sql:32970:  WHERE fmin = $1 AND fmax = $2
libchado-perl-1.31/schemas/1.11/default_schema.sql-32971-' LANGUAGE 'sql';
##############################################
libchado-perl-1.31/schemas/1.11/default_schema.sql-34526-    FROM phylonode
libchado-perl-1.31/schemas/1.11/default_schema.sql:34527:    WHERE parent_phylonode_id = $1
libchado-perl-1.31/schemas/1.11/default_schema.sql-34528-'
##############################################
libchado-perl-1.31/schemas/1.11/default_schema.sql-36420-FROM cvterm s, feature_cvterm fs
libchado-perl-1.31/schemas/1.11/default_schema.sql:36421:WHERE fs.feature_id= $1 AND fs.cvterm_id = s.cvterm_id
libchado-perl-1.31/schemas/1.11/default_schema.sql-36422-UNION
##############################################
libchado-perl-1.31/schemas/1.11/default_schema.sql-36424-FROM dbxref s, feature_dbxref fs, db d
libchado-perl-1.31/schemas/1.11/default_schema.sql:36425:WHERE fs.feature_id= $1 AND fs.dbxref_id = s.dbxref_id AND s.db_id = d.db_id
libchado-perl-1.31/schemas/1.11/default_schema.sql-36426---UNION
##############################################
libchado-perl-1.31/schemas/1.11/default_schema.sql-36428---FROM expression s, feature_expression fs
libchado-perl-1.31/schemas/1.11/default_schema.sql:36429:--WHERE fs.feature_id= $1 AND fs.expression_id = s.expression_id
libchado-perl-1.31/schemas/1.11/default_schema.sql-36430---UNION
##############################################
libchado-perl-1.31/schemas/1.11/default_schema.sql-36432---FROM gcontext g, feature_gcontext fg
libchado-perl-1.31/schemas/1.11/default_schema.sql:36433:--WHERE fg.feature_id= $1 AND g.gcontext_id = fg.gcontext_id
libchado-perl-1.31/schemas/1.11/default_schema.sql-36434---UNION
##############################################
libchado-perl-1.31/schemas/1.11/default_schema.sql-36436---FROM genotype s, feature_genotype fs
libchado-perl-1.31/schemas/1.11/default_schema.sql:36437:--WHERE fs.feature_id= $1 AND fs.genotype_id = s.genotype_id
libchado-perl-1.31/schemas/1.11/default_schema.sql-36438---UNION
##############################################
libchado-perl-1.31/schemas/1.11/default_schema.sql-36440---FROM phenotype s, feature_phenotype fs
libchado-perl-1.31/schemas/1.11/default_schema.sql:36441:--WHERE fs.feature_id= $1 AND fs.phenotype_id = s.phenotype_id
libchado-perl-1.31/schemas/1.11/default_schema.sql-36442-UNION
##############################################
libchado-perl-1.31/schemas/1.11/default_schema.sql-36444-FROM synonym s, feature_synonym fs
libchado-perl-1.31/schemas/1.11/default_schema.sql:36445:WHERE fs.feature_id= $1 AND fs.synonym_id = s.synonym_id
libchado-perl-1.31/schemas/1.11/default_schema.sql-36446-UNION
##############################################
libchado-perl-1.31/schemas/1.11/default_schema.sql-36448-FROM featureprop fp, cvterm cv
libchado-perl-1.31/schemas/1.11/default_schema.sql:36449:WHERE fp.feature_id= $1 AND fp.type_id = cv.cvterm_id 
libchado-perl-1.31/schemas/1.11/default_schema.sql-36450-UNION
##############################################
libchado-perl-1.31/schemas/1.11/default_schema.sql-36452-FROM pub s, feature_pub fs
libchado-perl-1.31/schemas/1.11/default_schema.sql:36453:WHERE fs.feature_id= $1 AND fs.pub_id = s.pub_id
libchado-perl-1.31/schemas/1.11/default_schema.sql-36454-'
##############################################
libchado-perl-1.31/schemas/1.11-1.21/diff.sql-140- );
libchado-perl-1.31/schemas/1.11-1.21/diff.sql:141:COMMENT ON TABLE stock_relationship_cvterm is 'For germplasm maintenance and pedigree data, stock_relationship. type_id will record cvterms such as "is a female parent of", "a parent for mutation", "is a group_id of", "is a source_id of", etc The cvterms for higher categories such as "generative", "derivative" or "maintenance" can be stored in table stock_relationship_cvterm';
libchado-perl-1.31/schemas/1.11-1.21/diff.sql-142-
##############################################
libchado-perl-1.31/schemas/1.11-1.21/diff-94-> --- *** Any one of several small cytoplasmic RNA ***
libchado-perl-1.31/schemas/1.11-1.21/diff:95:> --- ***  molecules present in the cytoplasm and  ***
libchado-perl-1.31/schemas/1.11-1.21/diff-96-> --- *** sometimes nucleus of a eukaryote.        ***
##############################################
libchado-perl-1.31/schemas/1.11-1.21/diff-10653-< );
libchado-perl-1.31/schemas/1.11-1.21/diff:10654:< COMMENT ON TABLE stock_relationship_cvterm is 'For germplasm maintenance and pedigree data, stock_relationship. type_id will record cvterms such as "is a female parent of", "a parent for mutation", "is a group_id of", "is a source_id of", etc The cvterms for higher categories such as "generative", "derivative" or "maintenance" can be stored in table stock_relationship_cvterm';
libchado-perl-1.31/schemas/1.11-1.21/diff-10655-< 
##############################################
libchado-perl-1.31/schemas/1.11-1.21/diff-10805-> --FROM expression s, feature_expression fs
libchado-perl-1.31/schemas/1.11-1.21/diff:10806:> --WHERE fs.feature_id= $1 AND fs.expression_id = s.expression_id
libchado-perl-1.31/schemas/1.11-1.21/diff-10807-> --UNION
##############################################
libchado-perl-1.31/schemas/1.11-1.21/diff-10809-> --FROM gcontext g, feature_gcontext fg
libchado-perl-1.31/schemas/1.11-1.21/diff:10810:> --WHERE fg.feature_id= $1 AND g.gcontext_id = fg.gcontext_id
libchado-perl-1.31/schemas/1.11-1.21/diff-10811-> --UNION
##############################################
libchado-perl-1.31/schemas/1.11-1.21/diff-10813-> --FROM genotype s, feature_genotype fs
libchado-perl-1.31/schemas/1.11-1.21/diff:10814:> --WHERE fs.feature_id= $1 AND fs.genotype_id = s.genotype_id
libchado-perl-1.31/schemas/1.11-1.21/diff-10815-> --UNION
##############################################
libchado-perl-1.31/schemas/1.11-1.21/diff-10817-> --FROM phenotype s, feature_phenotype fs
libchado-perl-1.31/schemas/1.11-1.21/diff:10818:> --WHERE fs.feature_id= $1 AND fs.phenotype_id = s.phenotype_id
libchado-perl-1.31/schemas/1.11-1.21/diff-10819-41168c36443
##############################################
libchado-perl-1.31/schemas/1.1/default_schema.sql-1165-  FROM organism
libchado-perl-1.31/schemas/1.1/default_schema.sql:1166:  WHERE genus=$1
libchado-perl-1.31/schemas/1.1/default_schema.sql-1167-    AND species=$2
##############################################
libchado-perl-1.31/schemas/1.1/default_schema.sql-1173-  FROM organism
libchado-perl-1.31/schemas/1.1/default_schema.sql:1174:  WHERE genus=substring($1,1,position('' '' IN $1)-1)
libchado-perl-1.31/schemas/1.1/default_schema.sql-1175-    AND species=substring($1,position('' '' IN $1)+1)
##############################################
libchado-perl-1.31/schemas/1.1/default_schema.sql-1181-  FROM organism
libchado-perl-1.31/schemas/1.1/default_schema.sql:1182:  WHERE substr(genus,1,1)=substring($1,1,1)
libchado-perl-1.31/schemas/1.1/default_schema.sql-1183-    AND species=substring($1,position('' '' IN $1)+1)
##############################################
libchado-perl-1.31/schemas/1.1/default_schema.sql-2057-CREATE OR REPLACE FUNCTION translate_codon(TEXT,INT) RETURNS CHAR AS
libchado-perl-1.31/schemas/1.1/default_schema.sql:2058: 'SELECT aa FROM genetic_code.gencode_codon_aa WHERE codon=$1 AND gencode_id=$2'
libchado-perl-1.31/schemas/1.1/default_schema.sql-2059-LANGUAGE 'sql';
##############################################
libchado-perl-1.31/schemas/1.1/default_schema.sql-2373-  FROM cv INNER JOIN cvterm USING (cv_id)
libchado-perl-1.31/schemas/1.1/default_schema.sql:2374:  WHERE cvterm.name=$1 AND cv.name=''sequence''
libchado-perl-1.31/schemas/1.1/default_schema.sql-2375- ' LANGUAGE 'sql';
##############################################
libchado-perl-1.31/schemas/1.1/default_schema.sql-2380-  FROM cv INNER JOIN cvterm USING (cv_id)
libchado-perl-1.31/schemas/1.1/default_schema.sql:2381:  WHERE cvterm.name=$1 AND cv.name=''feature_property''
libchado-perl-1.31/schemas/1.1/default_schema.sql-2382- ' LANGUAGE 'sql';
##############################################
libchado-perl-1.31/schemas/1.1/default_schema.sql-2387-  FROM cv INNER JOIN cvterm USING (cv_id)
libchado-perl-1.31/schemas/1.1/default_schema.sql:2388:  WHERE cvterm.name=$1 AND cv.name=''relationship''
libchado-perl-1.31/schemas/1.1/default_schema.sql-2389- ' LANGUAGE 'sql';
##############################################
libchado-perl-1.31/schemas/1.1/default_schema.sql-2395-  FROM feature
libchado-perl-1.31/schemas/1.1/default_schema.sql:2396:  WHERE uniquename=$1
libchado-perl-1.31/schemas/1.1/default_schema.sql-2397-    AND type_id=get_feature_type_id($2)
##############################################
libchado-perl-1.31/schemas/1.1/default_schema.sql-2568---- *** eral small cytoplasmic RNA molecules pre ***
libchado-perl-1.31/schemas/1.1/default_schema.sql:2569:--- *** sent in the cytoplasm and sometimes nucl ***
libchado-perl-1.31/schemas/1.1/default_schema.sql-2570---- *** eus of a eukaryote.                      ***
##############################################
libchado-perl-1.31/schemas/1.1/default_schema.sql-2586---- *** Any one of several small cytoplasmic RNA ***
libchado-perl-1.31/schemas/1.1/default_schema.sql:2587:--- ***  molecules present in the cytoplasm and  ***
libchado-perl-1.31/schemas/1.1/default_schema.sql-2588---- *** sometimes nucleus of a eukaryote.        ***
##############################################
libchado-perl-1.31/schemas/1.1/default_schema.sql-32950-    AND g1.group_id = g2.group_id
libchado-perl-1.31/schemas/1.1/default_schema.sql:32951:    AND g1.srcfeature_id = (SELECT feature_id FROM feature WHERE uniquename = $3)
libchado-perl-1.31/schemas/1.1/default_schema.sql-32952-    AND boxquery($1, $2) @ boxrange(g1.fmin,g2.fmax)
##############################################
libchado-perl-1.31/schemas/1.1/default_schema.sql-32957-  FROM groupoverlaps($1,$2,$3)
libchado-perl-1.31/schemas/1.1/default_schema.sql:32958:  WHERE fmin <= $1 AND fmax >= $2
libchado-perl-1.31/schemas/1.1/default_schema.sql-32959-' LANGUAGE 'sql';
##############################################
libchado-perl-1.31/schemas/1.1/default_schema.sql-32963-  FROM groupoverlaps($1,$2,$3)
libchado-perl-1.31/schemas/1.1/default_schema.sql:32964:  WHERE fmin >= $1 AND fmax <= $2
libchado-perl-1.31/schemas/1.1/default_schema.sql-32965-' LANGUAGE 'sql';
##############################################
libchado-perl-1.31/schemas/1.1/default_schema.sql-32969-  FROM groupoverlaps($1,$2,$3)
libchado-perl-1.31/schemas/1.1/default_schema.sql:32970:  WHERE fmin = $1 AND fmax = $2
libchado-perl-1.31/schemas/1.1/default_schema.sql-32971-' LANGUAGE 'sql';
##############################################
libchado-perl-1.31/schemas/1.1/default_schema.sql-34526-    FROM phylonode
libchado-perl-1.31/schemas/1.1/default_schema.sql:34527:    WHERE parent_phylonode_id = $1
libchado-perl-1.31/schemas/1.1/default_schema.sql-34528-'
##############################################
libchado-perl-1.31/schemas/1.1/default_schema.sql-36420-FROM cvterm s, feature_cvterm fs
libchado-perl-1.31/schemas/1.1/default_schema.sql:36421:WHERE fs.feature_id= $1 AND fs.cvterm_id = s.cvterm_id
libchado-perl-1.31/schemas/1.1/default_schema.sql-36422-UNION
##############################################
libchado-perl-1.31/schemas/1.1/default_schema.sql-36424-FROM dbxref s, feature_dbxref fs, db d
libchado-perl-1.31/schemas/1.1/default_schema.sql:36425:WHERE fs.feature_id= $1 AND fs.dbxref_id = s.dbxref_id AND s.db_id = d.db_id
libchado-perl-1.31/schemas/1.1/default_schema.sql-36426---UNION
##############################################
libchado-perl-1.31/schemas/1.1/default_schema.sql-36428---FROM expression s, feature_expression fs
libchado-perl-1.31/schemas/1.1/default_schema.sql:36429:--WHERE fs.feature_id= $1 AND fs.expression_id = s.expression_id
libchado-perl-1.31/schemas/1.1/default_schema.sql-36430---UNION
##############################################
libchado-perl-1.31/schemas/1.1/default_schema.sql-36432---FROM gcontext g, feature_gcontext fg
libchado-perl-1.31/schemas/1.1/default_schema.sql:36433:--WHERE fg.feature_id= $1 AND g.gcontext_id = fg.gcontext_id
libchado-perl-1.31/schemas/1.1/default_schema.sql-36434---UNION
##############################################
libchado-perl-1.31/schemas/1.1/default_schema.sql-36436---FROM genotype s, feature_genotype fs
libchado-perl-1.31/schemas/1.1/default_schema.sql:36437:--WHERE fs.feature_id= $1 AND fs.genotype_id = s.genotype_id
libchado-perl-1.31/schemas/1.1/default_schema.sql-36438---UNION
##############################################
libchado-perl-1.31/schemas/1.1/default_schema.sql-36440---FROM phenotype s, feature_phenotype fs
libchado-perl-1.31/schemas/1.1/default_schema.sql:36441:--WHERE fs.feature_id= $1 AND fs.phenotype_id = s.phenotype_id
libchado-perl-1.31/schemas/1.1/default_schema.sql-36442-UNION
##############################################
libchado-perl-1.31/schemas/1.1/default_schema.sql-36444-FROM synonym s, feature_synonym fs
libchado-perl-1.31/schemas/1.1/default_schema.sql:36445:WHERE fs.feature_id= $1 AND fs.synonym_id = s.synonym_id
libchado-perl-1.31/schemas/1.1/default_schema.sql-36446-UNION
##############################################
libchado-perl-1.31/schemas/1.1/default_schema.sql-36448-FROM featureprop fp, cvterm cv
libchado-perl-1.31/schemas/1.1/default_schema.sql:36449:WHERE fp.feature_id= $1 AND fp.type_id = cv.cvterm_id 
libchado-perl-1.31/schemas/1.1/default_schema.sql-36450-UNION
##############################################
libchado-perl-1.31/schemas/1.1/default_schema.sql-36452-FROM pub s, feature_pub fs
libchado-perl-1.31/schemas/1.1/default_schema.sql:36453:WHERE fs.feature_id= $1 AND fs.pub_id = s.pub_id
libchado-perl-1.31/schemas/1.1/default_schema.sql-36454-'
##############################################
libchado-perl-1.31/schemas/1-1.2/diff.sql-521- );
libchado-perl-1.31/schemas/1-1.2/diff.sql:522:COMMENT ON TABLE stock_relationship_cvterm is 'For germplasm maintenance and pedigree data, stock_relationship. type_id will record cvterms such as "is a female parent of", "a parent for mutation", "is a group_id of", "is a source_id of", etc The cvterms for higher categories such as "generative", "derivative" or "maintenance" can be stored in table stock_relationship_cvterm';
libchado-perl-1.31/schemas/1-1.2/diff.sql-523-
##############################################
libchado-perl-1.31/schemas/generate_diff_dirs.pl-13-copy("../modules/default_schema.sql", $VERSION);
libchado-perl-1.31/schemas/generate_diff_dirs.pl:14:system("git add $VERSION");
libchado-perl-1.31/schemas/generate_diff_dirs.pl-15-
##############################################
libchado-perl-1.31/schemas/generate_diff_dirs.pl-26-        mkdir $newdir;
libchado-perl-1.31/schemas/generate_diff_dirs.pl:27:        system("touch $newdir/diff.sql");
libchado-perl-1.31/schemas/generate_diff_dirs.pl-28-        push @add_to_manifest, "schemas/$newdir/diff.sql";
libchado-perl-1.31/schemas/generate_diff_dirs.pl:29:        system("git add $newdir");
libchado-perl-1.31/schemas/generate_diff_dirs.pl-30-    }
##############################################
libchado-perl-1.31/debian/patches/setBinPathForBuilder-8-@@ -97,12 +97,12 @@
libchado-perl-1.31/debian/patches/setBinPathForBuilder:9:       my $result = `bin/gmod_add_organism.pl --name_only --common_name $db_org`;
libchado-perl-1.31/debian/patches/setBinPathForBuilder-10-       unless ($result) {
libchado-perl-1.31/debian/patches/setBinPathForBuilder-11-           print "Adding $db_org to the database...\n";
libchado-perl-1.31/debian/patches/setBinPathForBuilder:12:-          system('bin/gmod_add_organism.pl','--common_name',$db_org);
libchado-perl-1.31/debian/patches/setBinPathForBuilder:13:+          system('/usr/share/gmod/chado/bin/gmod_add_organism.pl','--common_name',$db_org);
libchado-perl-1.31/debian/patches/setBinPathForBuilder-14-       }  
##############################################
libchado-perl-1.31/debian/patches/setBinPathForBuilder-17-   #set the chado schema version in the database
libchado-perl-1.31/debian/patches/setBinPathForBuilder:18:-  system("gmod_chado_properties.pl --dbprofile $db_name --force --version $schema_version"); 
libchado-perl-1.31/debian/patches/setBinPathForBuilder:19:+  system("/usr/share/gmod/chado/bin/gmod_chado_properties.pl --dbprofile $db_name --force --version $schema_version"); 
libchado-perl-1.31/debian/patches/setBinPathForBuilder-20- 
##############################################
libchado-perl-1.31/debian/patches/setBinPathForBuilder-26-     print "Attempting schema update.\n";
libchado-perl-1.31/debian/patches/setBinPathForBuilder:27:-    system("gmod_update_chado.pl --dbprofile $db_name");
libchado-perl-1.31/debian/patches/setBinPathForBuilder:28:+    system("/usr/share/gmod/chado/bin/gmod_update_chado.pl --dbprofile $db_name");
libchado-perl-1.31/debian/patches/setBinPathForBuilder-29-   } 
##############################################
libchado-perl-1.31/.pc/fix_perl_headers/load/bin/bulk_load_gff3.PLS-618-) 
libchado-perl-1.31/.pc/fix_perl_headers/load/bin/bulk_load_gff3.PLS:619:# or ( system( 'pod2text', $0 ), exit -1 );
libchado-perl-1.31/.pc/fix_perl_headers/load/bin/bulk_load_gff3.PLS-620-or pod2usage(-verbose => 1, -exitval => 1);
##############################################
libchado-perl-1.31/.pc/fix_perl_headers/load/bin/load_gff3.PLS-840-      )
libchado-perl-1.31/.pc/fix_perl_headers/load/bin/load_gff3.PLS:841:      or ( system( 'pod2text', $0 ), exit -1 );
libchado-perl-1.31/.pc/fix_perl_headers/load/bin/load_gff3.PLS-842-
##############################################
libchado-perl-1.31/.pc/fix_perl_headers/load/bin/load_gff3.PLS-870-
libchado-perl-1.31/.pc/fix_perl_headers/load/bin/load_gff3.PLS:871:    my $linenumber = `grep -n "^>" $GFFFILE`;
libchado-perl-1.31/.pc/fix_perl_headers/load/bin/load_gff3.PLS-872-    if ( $linenumber =~ /^(\d+)/ ) {
libchado-perl-1.31/.pc/fix_perl_headers/load/bin/load_gff3.PLS-873-        $linenumber = $1;
libchado-perl-1.31/.pc/fix_perl_headers/load/bin/load_gff3.PLS:874:        system("tail -n +$linenumber $GFFFILE > $TMPFASTA");
libchado-perl-1.31/.pc/fix_perl_headers/load/bin/load_gff3.PLS-875-        $linenumber -= 1;
libchado-perl-1.31/.pc/fix_perl_headers/load/bin/load_gff3.PLS:876:        system("head -n $linenumber $GFFFILE > $TMPGFF");
libchado-perl-1.31/.pc/fix_perl_headers/load/bin/load_gff3.PLS-877-
##############################################
libchado-perl-1.31/.pc/force_SIMPLE/Makefile.PL-380-
libchado-perl-1.31/.pc/force_SIMPLE/Makefile.PL:381:    system("ant", "gmodrel", "-Dgmod.dir=$working_dir") == 0 or
libchado-perl-1.31/.pc/force_SIMPLE/Makefile.PL-382-        (warn "\n\n****************\nMoving tools from GMODTools directory faild; do you have ant installed?\n****************\n\n" && $ant = 0);
##############################################
libchado-perl-1.31/.pc/force_SIMPLE/Makefile.PL-465-if ($O{'SIMPLE'} =~ /^[Yy]/) {
libchado-perl-1.31/.pc/force_SIMPLE/Makefile.PL:466:    system(  $PERL, 'bin/AutoDBI.PL') == 0
libchado-perl-1.31/.pc/force_SIMPLE/Makefile.PL-467-        or die "unable to run bin/AutoDBI.PL: $!\n";
##############################################
libchado-perl-1.31/.pc/force_SIMPLE/Makefile.PL-492-
libchado-perl-1.31/.pc/force_SIMPLE/Makefile.PL:493:system( "$PERL load/Build.PL load_conf=$load_config; ./Build" ) == 0
libchado-perl-1.31/.pc/force_SIMPLE/Makefile.PL-494-    or die "unable to create Build from load/Build.PL: $!\n";
##############################################
libchado-perl-1.31/.pc/force_SIMPLE/Makefile.PL-768-rm_locks ::
libchado-perl-1.31/.pc/force_SIMPLE/Makefile.PL:769:	`find $LOCAL_TMP -name "*$DBNAME" -exec rm -f '{}' ';'`
libchado-perl-1.31/.pc/force_SIMPLE/Makefile.PL-770-
##############################################
libchado-perl-1.31/.pc/fix_spelling_manpage/lib/Bio/GMOD/DB/Adapter.pm-2525-  INSERT INTO dbxref (db_id,accession)
libchado-perl-1.31/.pc/fix_spelling_manpage/lib/Bio/GMOD/DB/Adapter.pm:2526:    VALUES ((select db_id from db where name='null'),'autocreated:$tag');
libchado-perl-1.31/.pc/fix_spelling_manpage/lib/Bio/GMOD/DB/Adapter.pm-2527-  INSERT INTO cvterm (cv_id,name,dbxref_id)
libchado-perl-1.31/.pc/fix_spelling_manpage/lib/Bio/GMOD/DB/Adapter.pm:2528:    VALUES ((select cv_id from cv where name='autocreated'), '$tag',
libchado-perl-1.31/.pc/fix_spelling_manpage/lib/Bio/GMOD/DB/Adapter.pm:2529:            (select dbxref_id from dbxref where accession='autocreated:$tag'));
libchado-perl-1.31/.pc/fix_spelling_manpage/lib/Bio/GMOD/DB/Adapter.pm-2530-
##############################################
libchado-perl-1.31/.pc/fix_spelling_manpage/lib/Bio/GMOD/DB/Adapter.pm-2547-  my $fh = $self->file_handles('delete');
libchado-perl-1.31/.pc/fix_spelling_manpage/lib/Bio/GMOD/DB/Adapter.pm:2548:  print $fh "DELETE FROM $table WHERE feature_id = $feature_id;\n";
libchado-perl-1.31/.pc/fix_spelling_manpage/lib/Bio/GMOD/DB/Adapter.pm-2549-  return;
##############################################
libchado-perl-1.31/.pc/fix_spelling_manpage/lib/Bio/GMOD/DB/Adapter.pm-2578-  my $len = length($string);
libchado-perl-1.31/.pc/fix_spelling_manpage/lib/Bio/GMOD/DB/Adapter.pm:2579:  print $fh "UPDATE feature set residues='$string', seqlen=$len WHERE feature_id=$feature_id;\n";
libchado-perl-1.31/.pc/fix_spelling_manpage/lib/Bio/GMOD/DB/Adapter.pm-2580-
##############################################
libchado-perl-1.31/.pc/fix_spelling_manpage/lib/Bio/GMOD/DB/Adapter.pm-2613-  my $len = length($string);
libchado-perl-1.31/.pc/fix_spelling_manpage/lib/Bio/GMOD/DB/Adapter.pm:2614:  print $fh "UPDATE feature set residues='$string',seqlen=$len WHERE feature_id=$feature_id;\n";
libchado-perl-1.31/.pc/fix_spelling_manpage/lib/Bio/GMOD/DB/Adapter.pm-2615-
##############################################
libchado-perl-1.31/.pc/fix_spelling_manpage/lib/Bio/GMOD/DB/Adapter.pm-3797-      
libchado-perl-1.31/.pc/fix_spelling_manpage/lib/Bio/GMOD/DB/Adapter.pm:3798:        my $sth = $self->dbh->prepare("SELECT cv_id FROM cv WHERE name='". $self->fp_cv()  ."'");
libchado-perl-1.31/.pc/fix_spelling_manpage/lib/Bio/GMOD/DB/Adapter.pm-3799-          # dgg: dropped  'autocreated' due to SO/auto conflicts for things like 'gene', 'chromosome'
##############################################
libchado-perl-1.31/.pc/fix_spelling_manpage/lib/Bio/GMOD/DB/Adapter.pm-3813-#       if (!$self->{const}{tried_fp_cv} and !$self->{const}{fp_cv_id}) {
libchado-perl-1.31/.pc/fix_spelling_manpage/lib/Bio/GMOD/DB/Adapter.pm:3814:#         my $sth = $self->dbh->prepare("SELECT cv_id FROM cv WHERE name='". $self->fp_cv  ."'");
libchado-perl-1.31/.pc/fix_spelling_manpage/lib/Bio/GMOD/DB/Adapter.pm-3815-#         $sth->execute;
##############################################
libchado-perl-1.31/.pc/fix_spelling_manpage/lib/Bio/GMOD/DB/Adapter.pm-4737-
libchado-perl-1.31/.pc/fix_spelling_manpage/lib/Bio/GMOD/DB/Adapter.pm:4738:    my $sth  = $dbh->prepare("SELECT distinct gffline FROM gff_sort_tmp WHERE refseq = id") or $self->throw();
libchado-perl-1.31/.pc/fix_spelling_manpage/lib/Bio/GMOD/DB/Adapter.pm-4739-    $sth->execute or $self->throw();
##############################################
libchado-perl-1.31/.pc/fix_spelling_manpage/lib/Bio/GMOD/DB/Adapter.pm-4758-
libchado-perl-1.31/.pc/fix_spelling_manpage/lib/Bio/GMOD/DB/Adapter.pm:4759:    $sth  = $dbh->prepare("SELECT distinct gffline,id FROM gff_sort_tmp WHERE parent is null and refseq != id order by id") or $self->throw();
libchado-perl-1.31/.pc/fix_spelling_manpage/lib/Bio/GMOD/DB/Adapter.pm-4760-    $sth->execute or $self->throw();
##############################################
libchado-perl-1.31/.pc/fix_spelling_manpage/lib/Bio/GMOD/Config2.pm-568-    $dir= "$dir/.."; ##NOT File::Basename::dirname($dir)."/..";
libchado-perl-1.31/.pc/fix_spelling_manpage/lib/Bio/GMOD/Config2.pm:569:    $dir=`cd "$dir" && pwd`; chomp($dir);
libchado-perl-1.31/.pc/fix_spelling_manpage/lib/Bio/GMOD/Config2.pm-570-    ##warn " _updir $dir\n" if $DEBUG;
##############################################
libchado-perl-1.31/.pc/fix_spelling_manpage/lib/Bio/GMOD/Bulkfiles/GenbankSubmitWriter.pm-235-
libchado-perl-1.31/.pc/fix_spelling_manpage/lib/Bio/GMOD/Bulkfiles/GenbankSubmitWriter.pm:236:  my $ok= system("$tbl2asn $opts ");
libchado-perl-1.31/.pc/fix_spelling_manpage/lib/Bio/GMOD/Bulkfiles/GenbankSubmitWriter.pm-237-  
##############################################
libchado-perl-1.31/.pc/fix_spelling_manpage/lib/Bio/GMOD/Bulkfiles/GenbankSubmitWriter.pm-489-#     my $to  = $mapname_pattern{$mp}->{to};
libchado-perl-1.31/.pc/fix_spelling_manpage/lib/Bio/GMOD/Bulkfiles/GenbankSubmitWriter.pm:490:#     if ($to =~ /\$/) { $name =~ s/$from/eval($to)/e; }
libchado-perl-1.31/.pc/fix_spelling_manpage/lib/Bio/GMOD/Bulkfiles/GenbankSubmitWriter.pm-491-#     else { $name =~ s/$from/$to/g; }
##############################################
libchado-perl-1.31/.pc/fix_spelling_manpage/lib/Bio/GMOD/Bulkfiles/GenbankSubmitWriter.pm-667-    my $to  = $mapattr_pattern{$mp}->{to};
libchado-perl-1.31/.pc/fix_spelling_manpage/lib/Bio/GMOD/Bulkfiles/GenbankSubmitWriter.pm:668:    if ($to =~ /\$/) { $attribute =~ s/$from/eval($to)/e; }
libchado-perl-1.31/.pc/fix_spelling_manpage/lib/Bio/GMOD/Bulkfiles/GenbankSubmitWriter.pm-669-    else { $attribute =~ s/$from/$to/g; }
##############################################
libchado-perl-1.31/.pc/fix_spelling_manpage/bin/gmod_gff3_preprocessor.pl-92-    'inheritance_tiers=i' => \$INHERITANCE_TIERS,
libchado-perl-1.31/.pc/fix_spelling_manpage/bin/gmod_gff3_preprocessor.pl:93:) or ( system( 'pod2text', $0 ), exit -1 );
libchado-perl-1.31/.pc/fix_spelling_manpage/bin/gmod_gff3_preprocessor.pl-94-
##############################################
libchado-perl-1.31/.pc/fix_spelling_manpage/bin/gmod_materialized_view_tool.pl-222-    'help'            => \$HELP,
libchado-perl-1.31/.pc/fix_spelling_manpage/bin/gmod_materialized_view_tool.pl:223:) or ( system( 'pod2text', $0 ), exit -1 );
libchado-perl-1.31/.pc/fix_spelling_manpage/bin/gmod_materialized_view_tool.pl-224-
libchado-perl-1.31/.pc/fix_spelling_manpage/bin/gmod_materialized_view_tool.pl:225:( system( 'pod2text', $0 ), exit -1 ) if $HELP;
libchado-perl-1.31/.pc/fix_spelling_manpage/bin/gmod_materialized_view_tool.pl-226-
##############################################
libchado-perl-1.31/.pc/fix_spelling_manpage/bin/gmod_materialized_view_tool.pl-289-else {
libchado-perl-1.31/.pc/fix_spelling_manpage/bin/gmod_materialized_view_tool.pl:290:    system( 'pod2text', $0 ), exit -1;
libchado-perl-1.31/.pc/fix_spelling_manpage/bin/gmod_materialized_view_tool.pl-291-}
##############################################
libchado-perl-1.31/.pc/fix_spelling_manpage/load/bin/bulk_load_gff3.PLS-618-) 
libchado-perl-1.31/.pc/fix_spelling_manpage/load/bin/bulk_load_gff3.PLS:619:# or ( system( 'pod2text', $0 ), exit -1 );
libchado-perl-1.31/.pc/fix_spelling_manpage/load/bin/bulk_load_gff3.PLS-620-or pod2usage(-verbose => 1, -exitval => 1);
##############################################
libchado-perl-1.31/.pc/fix_manpages/bin/gmod_make_cvtermpath.pl-187-my $cv_id;
libchado-perl-1.31/.pc/fix_manpages/bin/gmod_make_cvtermpath.pl:188:warn "select cv_id from cv where name = '$cvname'" if $verbose;
libchado-perl-1.31/.pc/fix_manpages/bin/gmod_make_cvtermpath.pl:189:my $sth_cv = $db->prepare("select cv_id from cv where name = '$cvname'");
libchado-perl-1.31/.pc/fix_manpages/bin/gmod_make_cvtermpath.pl-190-$sth_cv->execute;
##############################################
libchado-perl-1.31/.pc/fix_manpages/bin/gmod_make_cvtermpath.pl-202-
libchado-perl-1.31/.pc/fix_manpages/bin/gmod_make_cvtermpath.pl:203:my $sth_cvterm_relationship = $db->prepare("select subject_id,type_id,object_id from cvterm_relationship,cvterm where cvterm_relationship.subject_id = cvterm.cvterm_id and cvterm.cv_id = $cv_id");
libchado-perl-1.31/.pc/fix_manpages/bin/gmod_make_cvtermpath.pl-204-$sth_cvterm_relationship->execute;
##############################################
libchado-perl-1.31/.pc/setBinPathForBuilder/lib/Bio/Chado/Builder.pm-89-
libchado-perl-1.31/.pc/setBinPathForBuilder/lib/Bio/Chado/Builder.pm:90:  system( $sys_call ) == 0 or croak "Error executing '$sys_call': $?";
libchado-perl-1.31/.pc/setBinPathForBuilder/lib/Bio/Chado/Builder.pm-91-
##############################################
libchado-perl-1.31/.pc/setBinPathForBuilder/lib/Bio/Chado/Builder.pm-96-  if ($db_org and $db_org ne 'none' and ref $db_org ne 'HASH') {
libchado-perl-1.31/.pc/setBinPathForBuilder/lib/Bio/Chado/Builder.pm:97:      my $result = `bin/gmod_add_organism.pl --name_only --common_name $db_org`;
libchado-perl-1.31/.pc/setBinPathForBuilder/lib/Bio/Chado/Builder.pm-98-      unless ($result) {
libchado-perl-1.31/.pc/setBinPathForBuilder/lib/Bio/Chado/Builder.pm-99-          print "Adding $db_org to the database...\n";
libchado-perl-1.31/.pc/setBinPathForBuilder/lib/Bio/Chado/Builder.pm:100:          system('bin/gmod_add_organism.pl','--common_name',$db_org);
libchado-perl-1.31/.pc/setBinPathForBuilder/lib/Bio/Chado/Builder.pm-101-      }  
##############################################
libchado-perl-1.31/.pc/setBinPathForBuilder/lib/Bio/Chado/Builder.pm-104-  #set the chado schema version in the database
libchado-perl-1.31/.pc/setBinPathForBuilder/lib/Bio/Chado/Builder.pm:105:  system("gmod_chado_properties.pl --dbprofile $db_name --force --version $schema_version"); 
libchado-perl-1.31/.pc/setBinPathForBuilder/lib/Bio/Chado/Builder.pm-106-
##############################################
libchado-perl-1.31/.pc/setBinPathForBuilder/lib/Bio/Chado/Builder.pm-131-
libchado-perl-1.31/.pc/setBinPathForBuilder/lib/Bio/Chado/Builder.pm:132:  my $version = `gmod_chado_properties.pl --dbprofile $db_name --version`; 
libchado-perl-1.31/.pc/setBinPathForBuilder/lib/Bio/Chado/Builder.pm-133-  chomp $version;
##############################################
libchado-perl-1.31/.pc/setBinPathForBuilder/lib/Bio/Chado/Builder.pm-136-    print "Attempting schema update.\n";
libchado-perl-1.31/.pc/setBinPathForBuilder/lib/Bio/Chado/Builder.pm:137:    system("gmod_update_chado.pl --dbprofile $db_name");
libchado-perl-1.31/.pc/setBinPathForBuilder/lib/Bio/Chado/Builder.pm-138-  } 
##############################################
libchado-perl-1.31/.pc/setBinPathForBuilder/lib/Bio/Chado/Builder.pm-220-
libchado-perl-1.31/.pc/setBinPathForBuilder/lib/Bio/Chado/Builder.pm:221:      my $result = system( $sys_call );
libchado-perl-1.31/.pc/setBinPathForBuilder/lib/Bio/Chado/Builder.pm-222-      if ( $result != 0 ) { 
##############################################
libchado-perl-1.31/.pc/setBinPathForBuilder/lib/Bio/Chado/Builder.pm-345-
libchado-perl-1.31/.pc/setBinPathForBuilder/lib/Bio/Chado/Builder.pm:346:      my $result = system( $sys_call );
libchado-perl-1.31/.pc/setBinPathForBuilder/lib/Bio/Chado/Builder.pm-347-
##############################################
libchado-perl-1.31/.pc/setBinPathForBuilder/lib/Bio/Chado/Builder.pm-363-
libchado-perl-1.31/.pc/setBinPathForBuilder/lib/Bio/Chado/Builder.pm:364:      $result = system( $sys_call );
libchado-perl-1.31/.pc/setBinPathForBuilder/lib/Bio/Chado/Builder.pm-365-
##############################################
libchado-perl-1.31/.pc/setBinPathForBuilder/lib/Bio/Chado/Builder.pm-381-
libchado-perl-1.31/.pc/setBinPathForBuilder/lib/Bio/Chado/Builder.pm:382:        $result = system( $sys_call );
libchado-perl-1.31/.pc/setBinPathForBuilder/lib/Bio/Chado/Builder.pm-383-
##############################################
libchado-perl-1.31/.pc/setBinPathForBuilder/lib/Bio/Chado/Builder.pm-400-
libchado-perl-1.31/.pc/setBinPathForBuilder/lib/Bio/Chado/Builder.pm:401:        $result = system( $sys_call );
libchado-perl-1.31/.pc/setBinPathForBuilder/lib/Bio/Chado/Builder.pm-402-
##############################################
libchado-perl-1.31/.pc/setBinPathForBuilder/lib/Bio/Chado/Builder.pm-504-
libchado-perl-1.31/.pc/setBinPathForBuilder/lib/Bio/Chado/Builder.pm:505:        my $result = system( $sys_call );
libchado-perl-1.31/.pc/setBinPathForBuilder/lib/Bio/Chado/Builder.pm-506-
##############################################
libchado-perl-1.31/.pc/0001-Sort-generated-build.conf-for-reproducibility.patch/Makefile.PL-381-
libchado-perl-1.31/.pc/0001-Sort-generated-build.conf-for-reproducibility.patch/Makefile.PL:382:    system("ant", "gmodrel", "-Dgmod.dir=$working_dir") == 0 or
libchado-perl-1.31/.pc/0001-Sort-generated-build.conf-for-reproducibility.patch/Makefile.PL-383-        (warn "\n\n****************\nMoving tools from GMODTools directory faild; do you have ant installed?\n****************\n\n" && $ant = 0);
##############################################
libchado-perl-1.31/.pc/0001-Sort-generated-build.conf-for-reproducibility.patch/Makefile.PL-466-if ($O{'SIMPLE'} =~ /^[Yy]/) {
libchado-perl-1.31/.pc/0001-Sort-generated-build.conf-for-reproducibility.patch/Makefile.PL:467:    system(  $PERL, 'bin/AutoDBI.PL') == 0
libchado-perl-1.31/.pc/0001-Sort-generated-build.conf-for-reproducibility.patch/Makefile.PL-468-        or die "unable to run bin/AutoDBI.PL: $!\n";
##############################################
libchado-perl-1.31/.pc/0001-Sort-generated-build.conf-for-reproducibility.patch/Makefile.PL-493-
libchado-perl-1.31/.pc/0001-Sort-generated-build.conf-for-reproducibility.patch/Makefile.PL:494:system( "$PERL load/Build.PL load_conf=$load_config; ./Build" ) == 0
libchado-perl-1.31/.pc/0001-Sort-generated-build.conf-for-reproducibility.patch/Makefile.PL-495-    or die "unable to create Build from load/Build.PL: $!\n";
##############################################
libchado-perl-1.31/.pc/0001-Sort-generated-build.conf-for-reproducibility.patch/Makefile.PL-769-rm_locks ::
libchado-perl-1.31/.pc/0001-Sort-generated-build.conf-for-reproducibility.patch/Makefile.PL:770:	`find $LOCAL_TMP -name "*$DBNAME" -exec rm -f '{}' ';'`
libchado-perl-1.31/.pc/0001-Sort-generated-build.conf-for-reproducibility.patch/Makefile.PL-771-
##############################################
libchado-perl-1.31/.pc/0001-Sort-installed-configuration-file-for-reproducibilit.patch/install_util/conf_install.PLS-89-chmod 0755, $file or die "Can't reset permissions for $file: $!\n";
libchado-perl-1.31/.pc/0001-Sort-installed-configuration-file-for-reproducibilit.patch/install_util/conf_install.PLS:90:exec("$Config{'eunicefix'} $file") if $Config{'eunicefix'} ne ':';
libchado-perl-1.31/.pc/0001-Sort-installed-configuration-file-for-reproducibilit.patch/install_util/conf_install.PLS-91-chdir $origdir;
##############################################
libchado-perl-1.31/Makefile.PL-381-
libchado-perl-1.31/Makefile.PL:382:    system("ant", "gmodrel", "-Dgmod.dir=$working_dir") == 0 or
libchado-perl-1.31/Makefile.PL-383-        (warn "\n\n****************\nMoving tools from GMODTools directory faild; do you have ant installed?\n****************\n\n" && $ant = 0);
##############################################
libchado-perl-1.31/Makefile.PL-466-if ($O{'SIMPLE'} =~ /^[Yy]/) {
libchado-perl-1.31/Makefile.PL:467:    system(  $PERL, 'bin/AutoDBI.PL') == 0
libchado-perl-1.31/Makefile.PL-468-        or die "unable to run bin/AutoDBI.PL: $!\n";
##############################################
libchado-perl-1.31/Makefile.PL-493-
libchado-perl-1.31/Makefile.PL:494:system( "$PERL load/Build.PL load_conf=$load_config; ./Build" ) == 0
libchado-perl-1.31/Makefile.PL-495-    or die "unable to create Build from load/Build.PL: $!\n";
##############################################
libchado-perl-1.31/Makefile.PL-769-rm_locks ::
libchado-perl-1.31/Makefile.PL:770:	`find $LOCAL_TMP -name "*$DBNAME" -exec rm -f '{}' ';'`
libchado-perl-1.31/Makefile.PL-771-