===========================================================
.___ __ __
_________________ __ __ __| _/|__|/ |_
/ ___\_` __ \__ \ | | \/ __ | | \\_ __\
/ /_/ > | \// __ \| | / /_/ | | || |
\___ /|__| (____ /____/\____ | |__||__|
/_____/ \/ \/
grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
libtfbs-perl-0.7.1/Makefile-884- -e "@all = keys %{ maniread() };" \
libtfbs-perl-0.7.1/Makefile:885: -e "print(qq{Executing $(CI) @all\n}); system(qq{$(CI) @all});" \
libtfbs-perl-0.7.1/Makefile:886: -e "print(qq{Executing $(RCS_LABEL) ...\n}); system(qq{$(RCS_LABEL) @all});"
libtfbs-perl-0.7.1/Makefile-887-
##############################################
libtfbs-perl-0.7.1/Makefile.old-879- -e "@all = keys %{ maniread() };" \
libtfbs-perl-0.7.1/Makefile.old:880: -e "print(qq{Executing $(CI) @all\n}); system(qq{$(CI) @all});" \
libtfbs-perl-0.7.1/Makefile.old:881: -e "print(qq{Executing $(RCS_LABEL) ...\n}); system(qq{$(RCS_LABEL) @all});"
libtfbs-perl-0.7.1/Makefile.old-882-
##############################################
libtfbs-perl-0.7.1/TFBS/DB/FlatFileDir.pm-288- my $ucmt = uc $mt;
libtfbs-perl-0.7.1/TFBS/DB/FlatFileDir.pm:289: my $matrixstring =`cat $DIR/$ID.$mt`;
libtfbs-perl-0.7.1/TFBS/DB/FlatFileDir.pm-290-
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR.pm-410- qq!SELECT distinct BASE_ID FROM MATRIX
libtfbs-perl-0.7.1/TFBS/DB/JASPAR.pm:411: WHERE NAME="$name"!
libtfbs-perl-0.7.1/TFBS/DB/JASPAR.pm-412- );
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR.pm-620- ) {
libtfbs-perl-0.7.1/TFBS/DB/JASPAR.pm:621: $self->dbh->do("DELETE from $table where ID=$q_ID");
libtfbs-perl-0.7.1/TFBS/DB/JASPAR.pm-622- }
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR.pm-706- qq! SELECT BASE_ID, VERSION, NAME, LOG_P_1ST_ORDER, LOG_P_DETAILED,
libtfbs-perl-0.7.1/TFBS/DB/JASPAR.pm:707: EXPERIMENT_NAME FROM TFFM WHERE MATRIX_BASE_ID = "$matrix_base_id"
libtfbs-perl-0.7.1/TFBS/DB/JASPAR.pm-708- AND MATRIX_VERSION = "$matrix_version" !
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR.pm-786- my $sth = $self->dbh->prepare(
libtfbs-perl-0.7.1/TFBS/DB/JASPAR.pm:787: qq!SELECT distinct BASE_ID FROM TFFM WHERE NAME="$name"!
libtfbs-perl-0.7.1/TFBS/DB/JASPAR.pm-788- );
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR.pm-892- my $sth = $self->dbh->prepare(
libtfbs-perl-0.7.1/TFBS/DB/JASPAR.pm:893: qq! select count(*) from MATRIX where VERSION=$version
libtfbs-perl-0.7.1/TFBS/DB/JASPAR.pm-894- and BASE_ID= "$base_id" and collection="$collection" !
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR.pm-1196- "SELECT val FROM MATRIX_DATA
libtfbs-perl-0.7.1/TFBS/DB/JASPAR.pm:1197: WHERE ID=$qID AND row='$base' ORDER BY col"
libtfbs-perl-0.7.1/TFBS/DB/JASPAR.pm-1198- );
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR.pm-1213- qq!SELECT VERSION FROM MATRIX
libtfbs-perl-0.7.1/TFBS/DB/JASPAR.pm:1214: WHERE BASE_ID="$base_ID"
libtfbs-perl-0.7.1/TFBS/DB/JASPAR.pm-1215- ORDER BY VERSION DESC LIMIT 1!
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR.pm-1228- qq!SELECT ID FROM MATRIX
libtfbs-perl-0.7.1/TFBS/DB/JASPAR.pm:1229: WHERE BASE_ID="$base_ID" AND VERSION="$version"!
libtfbs-perl-0.7.1/TFBS/DB/JASPAR.pm-1230- );
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR.pm-1247- qq!SELECT BASE_ID,VERSION, COLLECTION,NAME FROM MATRIX
libtfbs-perl-0.7.1/TFBS/DB/JASPAR.pm:1248: WHERE ID="$int_id"!
libtfbs-perl-0.7.1/TFBS/DB/JASPAR.pm-1249- );
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR.pm-1254- # get species
libtfbs-perl-0.7.1/TFBS/DB/JASPAR.pm:1255: ##$sth=$self->dbh->prepare(qq!SELECT TAX_ID FROM MATRIX_SPECIES WHERE ID="$int_id"!);
libtfbs-perl-0.7.1/TFBS/DB/JASPAR.pm-1256- $sth = $self->dbh->prepare(
libtfbs-perl-0.7.1/TFBS/DB/JASPAR.pm:1257: qq!SELECT GROUP_CONCAT(TAX_ID SEPARATOR ', ') as TAX_ID FROM MATRIX_SPECIES WHERE ID="$int_id"!
libtfbs-perl-0.7.1/TFBS/DB/JASPAR.pm-1258- );
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR.pm-1268- # get acc
libtfbs-perl-0.7.1/TFBS/DB/JASPAR.pm:1269: ##$sth=$self->dbh->prepare(qq!SELECT ACC FROM MATRIX_PROTEIN WHERE ID="$int_id"!);
libtfbs-perl-0.7.1/TFBS/DB/JASPAR.pm-1270- $sth = $self->dbh->prepare(
libtfbs-perl-0.7.1/TFBS/DB/JASPAR.pm:1271: qq!SELECT GROUP_CONCAT(ACC SEPARATOR ', ') as ACC FROM MATRIX_PROTEIN WHERE ID="$int_id"!
libtfbs-perl-0.7.1/TFBS/DB/JASPAR.pm-1272- );
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR.pm-1284- $sth = $self->dbh->prepare(
libtfbs-perl-0.7.1/TFBS/DB/JASPAR.pm:1285: qq{SELECT TAG, VAL FROM MATRIX_ANNOTATION WHERE ID = "$int_id" });
libtfbs-perl-0.7.1/TFBS/DB/JASPAR.pm-1286- $sth->execute();
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR.pm-1598- qq! select count(*) from MATRIX
libtfbs-perl-0.7.1/TFBS/DB/JASPAR.pm:1599: where BASE_ID= (SELECT BASE_ID from MATRIX where ID=$int_id)
libtfbs-perl-0.7.1/TFBS/DB/JASPAR.pm:1600: AND VERSION>(SELECT VERSION from MATRIX where ID=$int_id) !
libtfbs-perl-0.7.1/TFBS/DB/JASPAR.pm-1601- );
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR.pm-1614- qq!SELECT VERSION FROM TFFM
libtfbs-perl-0.7.1/TFBS/DB/JASPAR.pm:1615: WHERE BASE_ID="$base_ID"
libtfbs-perl-0.7.1/TFBS/DB/JASPAR.pm-1616- ORDER BY VERSION DESC LIMIT 1!
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR.pm-1632- qq!SELECT ID FROM TFFM
libtfbs-perl-0.7.1/TFBS/DB/JASPAR.pm:1633: WHERE BASE_ID="$base_ID" AND VERSION="$version"!
libtfbs-perl-0.7.1/TFBS/DB/JASPAR.pm-1634- );
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR.pm-1647- LOG_P_1ST_ORDER, LOG_P_DETAILED, EXPERIMENT_NAME FROM TFFM
libtfbs-perl-0.7.1/TFBS/DB/JASPAR.pm:1648: WHERE ID = "$int_id" !
libtfbs-perl-0.7.1/TFBS/DB/JASPAR.pm-1649- );
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR.pm-1695- qq! select count(*) from TFFM
libtfbs-perl-0.7.1/TFBS/DB/JASPAR.pm:1696: where BASE_ID = (SELECT BASE_ID from TFFM where ID = $int_id)
libtfbs-perl-0.7.1/TFBS/DB/JASPAR.pm:1697: AND VERSION > (SELECT VERSION from TFFM where ID = $int_id) !
libtfbs-perl-0.7.1/TFBS/DB/JASPAR.pm-1698- );
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR2.pm-556- {
libtfbs-perl-0.7.1/TFBS/DB/JASPAR2.pm:557: $self->dbh->do("DELETE from $table where ID=$q_ID");
libtfbs-perl-0.7.1/TFBS/DB/JASPAR2.pm-558- }
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR2.pm-675- ("SELECT $dbname{$mt} FROM matrix_data
libtfbs-perl-0.7.1/TFBS/DB/JASPAR2.pm:676: WHERE ID=$qID AND base='$base' ORDER BY position");
libtfbs-perl-0.7.1/TFBS/DB/JASPAR2.pm-677- $sth->execute;
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR2.pm-691- my $sth = $self->dbh->prepare
libtfbs-perl-0.7.1/TFBS/DB/JASPAR2.pm:692: ("SELECT DISTINCT $retr_field from $table WHERE $search_field = $q_value and $retr_field <> \"\" ORDER BY $retr_field");
libtfbs-perl-0.7.1/TFBS/DB/JASPAR2.pm-693- $sth->execute;
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR4.pm-323- # get type of matrix
libtfbs-perl-0.7.1/TFBS/DB/JASPAR4.pm:324: my $sth=$self->dbh->prepare(qq{SELECT type FROM MATRIX_INFO WHERE ID = '$ID'});
libtfbs-perl-0.7.1/TFBS/DB/JASPAR4.pm-325- $sth->execute();
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR4.pm-329- # get reast of annotation as tags
libtfbs-perl-0.7.1/TFBS/DB/JASPAR4.pm:330: $sth=$self->dbh->prepare(qq{SELECT tag, val FROM MATRIX_ANNOTATION WHERE ID = '$ID' });
libtfbs-perl-0.7.1/TFBS/DB/JASPAR4.pm-331- $sth->execute();
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR4.pm-541- {
libtfbs-perl-0.7.1/TFBS/DB/JASPAR4.pm:542: $self->dbh->do("DELETE from $table where ID=$q_ID");
libtfbs-perl-0.7.1/TFBS/DB/JASPAR4.pm-543- }
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR4.pm-721- ("SELECT val FROM MATRIX_DATA
libtfbs-perl-0.7.1/TFBS/DB/JASPAR4.pm:722: WHERE ID=$qID AND row='$base' ORDER BY col");
libtfbs-perl-0.7.1/TFBS/DB/JASPAR4.pm-723- $sth->execute;
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR5.pm-370- my $sth=$self->dbh->prepare(qq!SELECT distinct BASE_ID FROM MATRIX
libtfbs-perl-0.7.1/TFBS/DB/JASPAR5.pm:371: WHERE NAME="$name"!);
libtfbs-perl-0.7.1/TFBS/DB/JASPAR5.pm-372- $sth->execute();
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR5.pm-580- {
libtfbs-perl-0.7.1/TFBS/DB/JASPAR5.pm:581: $self->dbh->do("DELETE from $table where ID=$q_ID");
libtfbs-perl-0.7.1/TFBS/DB/JASPAR5.pm-582- }
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR5.pm-665- my $sth = $self->dbh->prepare
libtfbs-perl-0.7.1/TFBS/DB/JASPAR5.pm:666: (qq! select count(*) from MATRIX where VERSION=$version and BASE_ID= "$base_id"and collection="$collection" !);
libtfbs-perl-0.7.1/TFBS/DB/JASPAR5.pm-667- $sth->execute;
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR5.pm-880- ("SELECT val FROM MATRIX_DATA
libtfbs-perl-0.7.1/TFBS/DB/JASPAR5.pm:881: WHERE ID=$qID AND row='$base' ORDER BY col");
libtfbs-perl-0.7.1/TFBS/DB/JASPAR5.pm-882- $sth->execute;
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR5.pm-896- (qq!SELECT VERSION FROM MATRIX
libtfbs-perl-0.7.1/TFBS/DB/JASPAR5.pm:897: WHERE BASE_ID="$base_ID"
libtfbs-perl-0.7.1/TFBS/DB/JASPAR5.pm-898- ORDER BY VERSION DESC LIMIT 1!);
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR5.pm-909- (qq!SELECT ID FROM MATRIX
libtfbs-perl-0.7.1/TFBS/DB/JASPAR5.pm:910: WHERE BASE_ID="$base_ID" AND VERSION="$version"!);
libtfbs-perl-0.7.1/TFBS/DB/JASPAR5.pm-911- $sth->execute;
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR5.pm-926- #get remaining data in the matrix table: name, collection
libtfbs-perl-0.7.1/TFBS/DB/JASPAR5.pm:927: my $sth=$self->dbh->prepare(qq!SELECT BASE_ID,VERSION, COLLECTION,NAME FROM MATRIX WHERE ID="$int_id"!);
libtfbs-perl-0.7.1/TFBS/DB/JASPAR5.pm-928- $sth->execute();
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR5.pm-931- # get species
libtfbs-perl-0.7.1/TFBS/DB/JASPAR5.pm:932: $sth=$self->dbh->prepare(qq!SELECT TAX_ID FROM MATRIX_SPECIES WHERE ID="$int_id"!);
libtfbs-perl-0.7.1/TFBS/DB/JASPAR5.pm-933- $sth->execute();
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR5.pm-939- # get acc
libtfbs-perl-0.7.1/TFBS/DB/JASPAR5.pm:940: $sth=$self->dbh->prepare(qq!SELECT ACC FROM MATRIX_PROTEIN WHERE ID="$int_id"!);
libtfbs-perl-0.7.1/TFBS/DB/JASPAR5.pm-941- $sth->execute();
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR5.pm-948- my %tags;
libtfbs-perl-0.7.1/TFBS/DB/JASPAR5.pm:949: $sth=$self->dbh->prepare(qq{SELECT TAG, VAL FROM MATRIX_ANNOTATION WHERE ID = "$int_id" });
libtfbs-perl-0.7.1/TFBS/DB/JASPAR5.pm-950- $sth->execute();
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR5.pm-1201- my $sth=$self->dbh->prepare( qq! select count(*) from MATRIX
libtfbs-perl-0.7.1/TFBS/DB/JASPAR5.pm:1202: where BASE_ID= (SELECT BASE_ID from MATRIX where ID=$int_id)
libtfbs-perl-0.7.1/TFBS/DB/JASPAR5.pm:1203: AND VERSION>(SELECT VERSION from MATRIX where ID=$int_id) !);
libtfbs-perl-0.7.1/TFBS/DB/JASPAR5.pm-1204- $sth->execute();
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR6.pm-373- my $sth=$self->dbh->prepare(qq!SELECT distinct BASE_ID FROM MATRIX
libtfbs-perl-0.7.1/TFBS/DB/JASPAR6.pm:374: WHERE NAME="$name"!);
libtfbs-perl-0.7.1/TFBS/DB/JASPAR6.pm-375- $sth->execute();
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR6.pm-591- {
libtfbs-perl-0.7.1/TFBS/DB/JASPAR6.pm:592: $self->dbh->do("DELETE from $table where ID=$q_ID");
libtfbs-perl-0.7.1/TFBS/DB/JASPAR6.pm-593- }
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR6.pm-676- my $sth = $self->dbh->prepare
libtfbs-perl-0.7.1/TFBS/DB/JASPAR6.pm:677: (qq! select count(*) from MATRIX where VERSION=$version and BASE_ID= "$base_id"and collection="$collection" !);
libtfbs-perl-0.7.1/TFBS/DB/JASPAR6.pm-678- $sth->execute;
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR6.pm-891- ("SELECT val FROM MATRIX_DATA
libtfbs-perl-0.7.1/TFBS/DB/JASPAR6.pm:892: WHERE ID=$qID AND row='$base' ORDER BY col");
libtfbs-perl-0.7.1/TFBS/DB/JASPAR6.pm-893- $sth->execute;
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR6.pm-907- (qq!SELECT VERSION FROM MATRIX
libtfbs-perl-0.7.1/TFBS/DB/JASPAR6.pm:908: WHERE BASE_ID="$base_ID"
libtfbs-perl-0.7.1/TFBS/DB/JASPAR6.pm-909- ORDER BY VERSION DESC LIMIT 1!);
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR6.pm-920- (qq!SELECT ID FROM MATRIX
libtfbs-perl-0.7.1/TFBS/DB/JASPAR6.pm:921: WHERE BASE_ID="$base_ID" AND VERSION="$version"!);
libtfbs-perl-0.7.1/TFBS/DB/JASPAR6.pm-922- $sth->execute;
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR6.pm-937- #get remaining data in the matrix table: name, collection
libtfbs-perl-0.7.1/TFBS/DB/JASPAR6.pm:938: my $sth=$self->dbh->prepare(qq!SELECT BASE_ID,VERSION, COLLECTION,NAME FROM MATRIX WHERE ID="$int_id"!);
libtfbs-perl-0.7.1/TFBS/DB/JASPAR6.pm-939- $sth->execute();
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR6.pm-945- # get species
libtfbs-perl-0.7.1/TFBS/DB/JASPAR6.pm:946: ##$sth=$self->dbh->prepare(qq!SELECT TAX_ID FROM MATRIX_SPECIES WHERE ID="$int_id"!);
libtfbs-perl-0.7.1/TFBS/DB/JASPAR6.pm:947: $sth=$self->dbh->prepare(qq!SELECT GROUP_CONCAT(TAX_ID SEPARATOR ', ') as TAX_ID FROM MATRIX_SPECIES WHERE ID="$int_id"!);
libtfbs-perl-0.7.1/TFBS/DB/JASPAR6.pm-948- $sth->execute();
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR6.pm-958- # get acc
libtfbs-perl-0.7.1/TFBS/DB/JASPAR6.pm:959: ##$sth=$self->dbh->prepare(qq!SELECT ACC FROM MATRIX_PROTEIN WHERE ID="$int_id"!);
libtfbs-perl-0.7.1/TFBS/DB/JASPAR6.pm:960: $sth=$self->dbh->prepare(qq!SELECT GROUP_CONCAT(ACC SEPARATOR ', ') as ACC FROM MATRIX_PROTEIN WHERE ID="$int_id"!);
libtfbs-perl-0.7.1/TFBS/DB/JASPAR6.pm-961- $sth->execute();
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR6.pm-973- my %tags;
libtfbs-perl-0.7.1/TFBS/DB/JASPAR6.pm:974: $sth=$self->dbh->prepare(qq{SELECT TAG, VAL FROM MATRIX_ANNOTATION WHERE ID = "$int_id" });
libtfbs-perl-0.7.1/TFBS/DB/JASPAR6.pm-975- $sth->execute();
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR6.pm-1283- my $sth=$self->dbh->prepare( qq! select count(*) from MATRIX
libtfbs-perl-0.7.1/TFBS/DB/JASPAR6.pm:1284: where BASE_ID= (SELECT BASE_ID from MATRIX where ID=$int_id)
libtfbs-perl-0.7.1/TFBS/DB/JASPAR6.pm:1285: AND VERSION>(SELECT VERSION from MATRIX where ID=$int_id) !);
libtfbs-perl-0.7.1/TFBS/DB/JASPAR6.pm-1286- $sth->execute();
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR7.pm-410- qq!SELECT distinct BASE_ID FROM MATRIX
libtfbs-perl-0.7.1/TFBS/DB/JASPAR7.pm:411: WHERE NAME="$name"!
libtfbs-perl-0.7.1/TFBS/DB/JASPAR7.pm-412- );
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR7.pm-620- ) {
libtfbs-perl-0.7.1/TFBS/DB/JASPAR7.pm:621: $self->dbh->do("DELETE from $table where ID=$q_ID");
libtfbs-perl-0.7.1/TFBS/DB/JASPAR7.pm-622- }
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR7.pm-706- qq! SELECT BASE_ID, VERSION, NAME, LOG_P_1ST_ORDER, LOG_P_DETAILED,
libtfbs-perl-0.7.1/TFBS/DB/JASPAR7.pm:707: EXPERIMENT_NAME FROM TFFM WHERE MATRIX_BASE_ID = "$matrix_base_id"
libtfbs-perl-0.7.1/TFBS/DB/JASPAR7.pm-708- AND MATRIX_VERSION = "$matrix_version" !
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR7.pm-786- my $sth = $self->dbh->prepare(
libtfbs-perl-0.7.1/TFBS/DB/JASPAR7.pm:787: qq!SELECT distinct BASE_ID FROM TFFM WHERE NAME="$name"!
libtfbs-perl-0.7.1/TFBS/DB/JASPAR7.pm-788- );
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR7.pm-892- my $sth = $self->dbh->prepare(
libtfbs-perl-0.7.1/TFBS/DB/JASPAR7.pm:893: qq! select count(*) from MATRIX where VERSION=$version
libtfbs-perl-0.7.1/TFBS/DB/JASPAR7.pm-894- and BASE_ID= "$base_id" and collection="$collection" !
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR7.pm-1196- "SELECT val FROM MATRIX_DATA
libtfbs-perl-0.7.1/TFBS/DB/JASPAR7.pm:1197: WHERE ID=$qID AND row='$base' ORDER BY col"
libtfbs-perl-0.7.1/TFBS/DB/JASPAR7.pm-1198- );
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR7.pm-1213- qq!SELECT VERSION FROM MATRIX
libtfbs-perl-0.7.1/TFBS/DB/JASPAR7.pm:1214: WHERE BASE_ID="$base_ID"
libtfbs-perl-0.7.1/TFBS/DB/JASPAR7.pm-1215- ORDER BY VERSION DESC LIMIT 1!
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR7.pm-1228- qq!SELECT ID FROM MATRIX
libtfbs-perl-0.7.1/TFBS/DB/JASPAR7.pm:1229: WHERE BASE_ID="$base_ID" AND VERSION="$version"!
libtfbs-perl-0.7.1/TFBS/DB/JASPAR7.pm-1230- );
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR7.pm-1247- qq!SELECT BASE_ID,VERSION, COLLECTION,NAME FROM MATRIX
libtfbs-perl-0.7.1/TFBS/DB/JASPAR7.pm:1248: WHERE ID="$int_id"!
libtfbs-perl-0.7.1/TFBS/DB/JASPAR7.pm-1249- );
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR7.pm-1254- # get species
libtfbs-perl-0.7.1/TFBS/DB/JASPAR7.pm:1255: ##$sth=$self->dbh->prepare(qq!SELECT TAX_ID FROM MATRIX_SPECIES WHERE ID="$int_id"!);
libtfbs-perl-0.7.1/TFBS/DB/JASPAR7.pm-1256- $sth = $self->dbh->prepare(
libtfbs-perl-0.7.1/TFBS/DB/JASPAR7.pm:1257: qq!SELECT GROUP_CONCAT(TAX_ID SEPARATOR ', ') as TAX_ID FROM MATRIX_SPECIES WHERE ID="$int_id"!
libtfbs-perl-0.7.1/TFBS/DB/JASPAR7.pm-1258- );
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR7.pm-1268- # get acc
libtfbs-perl-0.7.1/TFBS/DB/JASPAR7.pm:1269: ##$sth=$self->dbh->prepare(qq!SELECT ACC FROM MATRIX_PROTEIN WHERE ID="$int_id"!);
libtfbs-perl-0.7.1/TFBS/DB/JASPAR7.pm-1270- $sth = $self->dbh->prepare(
libtfbs-perl-0.7.1/TFBS/DB/JASPAR7.pm:1271: qq!SELECT GROUP_CONCAT(ACC SEPARATOR ', ') as ACC FROM MATRIX_PROTEIN WHERE ID="$int_id"!
libtfbs-perl-0.7.1/TFBS/DB/JASPAR7.pm-1272- );
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR7.pm-1284- $sth = $self->dbh->prepare(
libtfbs-perl-0.7.1/TFBS/DB/JASPAR7.pm:1285: qq{SELECT TAG, VAL FROM MATRIX_ANNOTATION WHERE ID = "$int_id" });
libtfbs-perl-0.7.1/TFBS/DB/JASPAR7.pm-1286- $sth->execute();
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR7.pm-1598- qq! select count(*) from MATRIX
libtfbs-perl-0.7.1/TFBS/DB/JASPAR7.pm:1599: where BASE_ID= (SELECT BASE_ID from MATRIX where ID=$int_id)
libtfbs-perl-0.7.1/TFBS/DB/JASPAR7.pm:1600: AND VERSION>(SELECT VERSION from MATRIX where ID=$int_id) !
libtfbs-perl-0.7.1/TFBS/DB/JASPAR7.pm-1601- );
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR7.pm-1614- qq!SELECT VERSION FROM TFFM
libtfbs-perl-0.7.1/TFBS/DB/JASPAR7.pm:1615: WHERE BASE_ID="$base_ID"
libtfbs-perl-0.7.1/TFBS/DB/JASPAR7.pm-1616- ORDER BY VERSION DESC LIMIT 1!
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR7.pm-1632- qq!SELECT ID FROM TFFM
libtfbs-perl-0.7.1/TFBS/DB/JASPAR7.pm:1633: WHERE BASE_ID="$base_ID" AND VERSION="$version"!
libtfbs-perl-0.7.1/TFBS/DB/JASPAR7.pm-1634- );
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR7.pm-1649- LOG_P_1ST_ORDER, LOG_P_DETAILED, EXPERIMENT_NAME FROM TFFM
libtfbs-perl-0.7.1/TFBS/DB/JASPAR7.pm:1650: WHERE ID = "$int_id" !
libtfbs-perl-0.7.1/TFBS/DB/JASPAR7.pm-1651- );
##############################################
libtfbs-perl-0.7.1/TFBS/DB/JASPAR7.pm-1697- qq! select count(*) from TFFM
libtfbs-perl-0.7.1/TFBS/DB/JASPAR7.pm:1698: where BASE_ID = (SELECT BASE_ID from TFFM where ID = $int_id)
libtfbs-perl-0.7.1/TFBS/DB/JASPAR7.pm:1699: AND VERSION > (SELECT VERSION from TFFM where ID = $int_id) !
libtfbs-perl-0.7.1/TFBS/DB/JASPAR7.pm-1700- );
##############################################
libtfbs-perl-0.7.1/TFBS/Matrix.pm-285- my $DIR = $self->{dbh};
libtfbs-perl-0.7.1/TFBS/Matrix.pm:286: $self->set_matrix(scalar `cat $DIR/$ID.pwm`); # FIXME - temporary
libtfbs-perl-0.7.1/TFBS/Matrix.pm-287-
##############################################
libtfbs-perl-0.7.1/TFBS/Matrix/Alignment.pm-130-
libtfbs-perl-0.7.1/TFBS/Matrix/Alignment.pm:131: foreach (`$args{'-binary'} $file1 $file2 $self->{'_open_penalty'} $self->{'_ext_penalty'}`){
libtfbs-perl-0.7.1/TFBS/Matrix/Alignment.pm-132- # my @pfm2_string;
##############################################
libtfbs-perl-0.7.1/TFBS/Matrix/PWM.pm-412- my @search_result_lines =
libtfbs-perl-0.7.1/TFBS/Matrix/PWM.pm:413: `$PWM_SEARCH $pwmfile $fastafile $threshold -n $TFname -c $TFclass`;
libtfbs-perl-0.7.1/TFBS/Matrix/PWM.pm-414- foreach (@search_result_lines) {
##############################################
libtfbs-perl-0.7.1/TFBS/PatternGen/AnnSpec.pm-124- # print STDERR "$command_line\n";
libtfbs-perl-0.7.1/TFBS/PatternGen/AnnSpec.pm:125: my $resultstring = `$command_line`;
libtfbs-perl-0.7.1/TFBS/PatternGen/AnnSpec.pm-126- print "$resultstring\n";
##############################################
libtfbs-perl-0.7.1/TFBS/PatternGen/Elph.pm-124-
libtfbs-perl-0.7.1/TFBS/PatternGen/Elph.pm:125: my $resultstring = `$command_line`;
libtfbs-perl-0.7.1/TFBS/PatternGen/Elph.pm-126- $self->_parse_elph_output($resultstring,$command_line);
##############################################
libtfbs-perl-0.7.1/TFBS/PatternGen/Gibbs.pm-130-
libtfbs-perl-0.7.1/TFBS/PatternGen/Gibbs.pm:131: my $resultstring = `$command_line`;
libtfbs-perl-0.7.1/TFBS/PatternGen/Gibbs.pm-132- $self->_parse_Gibbs_output($resultstring);
##############################################
libtfbs-perl-0.7.1/TFBS/PatternGen/MEME.pm-131-# print STDERR "$command_line\n";
libtfbs-perl-0.7.1/TFBS/PatternGen/MEME.pm:132: my $resultstring = `$command_line`;
libtfbs-perl-0.7.1/TFBS/PatternGen/MEME.pm-133- # print STDERR $resultstring;
##############################################
libtfbs-perl-0.7.1/TFBS/PatternGen/YMF.pm-131-# system $command;
libtfbs-perl-0.7.1/TFBS/PatternGen/YMF.pm:132:# `$command`;
libtfbs-perl-0.7.1/TFBS/PatternGen/YMF.pm-133-# system 'ls -ltr';
##############################################
libtfbs-perl-0.7.1/TFBS/PatternGen/YMF.pm-146-# print STDERR "cd $dir;$command_line\n";
libtfbs-perl-0.7.1/TFBS/PatternGen/YMF.pm:147: my $resultstring = `cd $dir;$command_line`;
libtfbs-perl-0.7.1/TFBS/PatternGen/YMF.pm-148- # print STDERR $resultstring;
##############################################
libtfbs-perl-0.7.1/TFBS/PatternGen/YMF.pm-187- #print $command;
libtfbs-perl-0.7.1/TFBS/PatternGen/YMF.pm:188: `$command`;# or die "could not unlink $!";
libtfbs-perl-0.7.1/TFBS/PatternGen/YMF.pm-189-# return
##############################################
libtfbs-perl-0.7.1/TFBS/Run/ConservationProfileGenerator.pm-156- my $command = join " ", $prog, @cl_args;
libtfbs-perl-0.7.1/TFBS/Run/ConservationProfileGenerator.pm:157: my @output_lines = `echo "$alnstring" | $command`;
libtfbs-perl-0.7.1/TFBS/Run/ConservationProfileGenerator.pm-158-
##############################################
libtfbs-perl-0.7.1/TFBS/MatrixSet.pm-720- $args .= "$_ $args{$_} " for (keys(%args));
libtfbs-perl-0.7.1/TFBS/MatrixSet.pm:721: my @output = `$path/STAMP -ch $args -out $fh`;
libtfbs-perl-0.7.1/TFBS/MatrixSet.pm-722-
##############################################
libtfbs-perl-0.7.1/blib/lib/TFBS/DB/FlatFileDir.pm-288- my $ucmt = uc $mt;
libtfbs-perl-0.7.1/blib/lib/TFBS/DB/FlatFileDir.pm:289: my $matrixstring =`cat $DIR/$ID.$mt`;
libtfbs-perl-0.7.1/blib/lib/TFBS/DB/FlatFileDir.pm-290-
##############################################
libtfbs-perl-0.7.1/blib/lib/TFBS/DB/JASPAR2.pm-556- {
libtfbs-perl-0.7.1/blib/lib/TFBS/DB/JASPAR2.pm:557: $self->dbh->do("DELETE from $table where ID=$q_ID");
libtfbs-perl-0.7.1/blib/lib/TFBS/DB/JASPAR2.pm-558- }
##############################################
libtfbs-perl-0.7.1/blib/lib/TFBS/DB/JASPAR2.pm-675- ("SELECT $dbname{$mt} FROM matrix_data
libtfbs-perl-0.7.1/blib/lib/TFBS/DB/JASPAR2.pm:676: WHERE ID=$qID AND base='$base' ORDER BY position");
libtfbs-perl-0.7.1/blib/lib/TFBS/DB/JASPAR2.pm-677- $sth->execute;
##############################################
libtfbs-perl-0.7.1/blib/lib/TFBS/DB/JASPAR2.pm-691- my $sth = $self->dbh->prepare
libtfbs-perl-0.7.1/blib/lib/TFBS/DB/JASPAR2.pm:692: ("SELECT DISTINCT $retr_field from $table WHERE $search_field = $q_value and $retr_field <> \"\" ORDER BY $retr_field");
libtfbs-perl-0.7.1/blib/lib/TFBS/DB/JASPAR2.pm-693- $sth->execute;
##############################################
libtfbs-perl-0.7.1/blib/lib/TFBS/DB/JASPAR4.pm-323- # get type of matrix
libtfbs-perl-0.7.1/blib/lib/TFBS/DB/JASPAR4.pm:324: my $sth=$self->dbh->prepare(qq{SELECT type FROM MATRIX_INFO WHERE ID = '$ID'});
libtfbs-perl-0.7.1/blib/lib/TFBS/DB/JASPAR4.pm-325- $sth->execute();
##############################################
libtfbs-perl-0.7.1/blib/lib/TFBS/DB/JASPAR4.pm-329- # get reast of annotation as tags
libtfbs-perl-0.7.1/blib/lib/TFBS/DB/JASPAR4.pm:330: $sth=$self->dbh->prepare(qq{SELECT tag, val FROM MATRIX_ANNOTATION WHERE ID = '$ID' });
libtfbs-perl-0.7.1/blib/lib/TFBS/DB/JASPAR4.pm-331- $sth->execute();
##############################################
libtfbs-perl-0.7.1/blib/lib/TFBS/DB/JASPAR4.pm-541- {
libtfbs-perl-0.7.1/blib/lib/TFBS/DB/JASPAR4.pm:542: $self->dbh->do("DELETE from $table where ID=$q_ID");
libtfbs-perl-0.7.1/blib/lib/TFBS/DB/JASPAR4.pm-543- }
##############################################
libtfbs-perl-0.7.1/blib/lib/TFBS/DB/JASPAR4.pm-721- ("SELECT val FROM MATRIX_DATA
libtfbs-perl-0.7.1/blib/lib/TFBS/DB/JASPAR4.pm:722: WHERE ID=$qID AND row='$base' ORDER BY col");
libtfbs-perl-0.7.1/blib/lib/TFBS/DB/JASPAR4.pm-723- $sth->execute;
##############################################
libtfbs-perl-0.7.1/blib/lib/TFBS/Matrix.pm-216- my $DIR = $self->{dbh};
libtfbs-perl-0.7.1/blib/lib/TFBS/Matrix.pm:217: $self->set_matrix(scalar `cat $DIR/$ID.pwm`); # FIXME - temporary
libtfbs-perl-0.7.1/blib/lib/TFBS/Matrix.pm-218-
##############################################
libtfbs-perl-0.7.1/blib/lib/TFBS/Matrix/PWM.pm-412- my @search_result_lines =
libtfbs-perl-0.7.1/blib/lib/TFBS/Matrix/PWM.pm:413: `$PWM_SEARCH $pwmfile $fastafile $threshold -n $TFname -c $TFclass`;
libtfbs-perl-0.7.1/blib/lib/TFBS/Matrix/PWM.pm-414- foreach (@search_result_lines) {
##############################################
libtfbs-perl-0.7.1/blib/lib/TFBS/PatternGen/AnnSpec.pm-124- # print STDERR "$command_line\n";
libtfbs-perl-0.7.1/blib/lib/TFBS/PatternGen/AnnSpec.pm:125: my $resultstring = `$command_line`;
libtfbs-perl-0.7.1/blib/lib/TFBS/PatternGen/AnnSpec.pm-126- # print STDERR $resultstring;
##############################################
libtfbs-perl-0.7.1/blib/lib/TFBS/PatternGen/Elph.pm-124-
libtfbs-perl-0.7.1/blib/lib/TFBS/PatternGen/Elph.pm:125: my $resultstring = `$command_line`;
libtfbs-perl-0.7.1/blib/lib/TFBS/PatternGen/Elph.pm-126- $self->_parse_elph_output($resultstring,$command_line);
##############################################
libtfbs-perl-0.7.1/blib/lib/TFBS/PatternGen/Gibbs.pm-130-
libtfbs-perl-0.7.1/blib/lib/TFBS/PatternGen/Gibbs.pm:131: my $resultstring = `$command_line`;
libtfbs-perl-0.7.1/blib/lib/TFBS/PatternGen/Gibbs.pm-132- $self->_parse_Gibbs_output($resultstring);
##############################################
libtfbs-perl-0.7.1/blib/lib/TFBS/PatternGen/MEME.pm-131-# print STDERR "$command_line\n";
libtfbs-perl-0.7.1/blib/lib/TFBS/PatternGen/MEME.pm:132: my $resultstring = `$command_line`;
libtfbs-perl-0.7.1/blib/lib/TFBS/PatternGen/MEME.pm-133- # print STDERR $resultstring;
##############################################
libtfbs-perl-0.7.1/blib/lib/TFBS/PatternGen/YMF.pm-131-# system $command;
libtfbs-perl-0.7.1/blib/lib/TFBS/PatternGen/YMF.pm:132:# `$command`;
libtfbs-perl-0.7.1/blib/lib/TFBS/PatternGen/YMF.pm-133-# system 'ls -ltr';
##############################################
libtfbs-perl-0.7.1/blib/lib/TFBS/PatternGen/YMF.pm-146-# print STDERR "cd $dir;$command_line\n";
libtfbs-perl-0.7.1/blib/lib/TFBS/PatternGen/YMF.pm:147: my $resultstring = `cd $dir;$command_line`;
libtfbs-perl-0.7.1/blib/lib/TFBS/PatternGen/YMF.pm-148- # print STDERR $resultstring;
##############################################
libtfbs-perl-0.7.1/blib/lib/TFBS/PatternGen/YMF.pm-187- #print $command;
libtfbs-perl-0.7.1/blib/lib/TFBS/PatternGen/YMF.pm:188: `$command`;# or die "could not unlink $!";
libtfbs-perl-0.7.1/blib/lib/TFBS/PatternGen/YMF.pm-189-# return
##############################################
libtfbs-perl-0.7.1/debian/tests/run-unit-test-5-if [ "$ADTTMP" = "" ] ; then
libtfbs-perl-0.7.1/debian/tests/run-unit-test:6: ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
libtfbs-perl-0.7.1/debian/tests/run-unit-test-7-fi
##############################################
libtfbs-perl-0.7.1/.pc/spelling-errors.patch/TFBS/PatternGen/YMF.pm-131-# system $command;
libtfbs-perl-0.7.1/.pc/spelling-errors.patch/TFBS/PatternGen/YMF.pm:132:# `$command`;
libtfbs-perl-0.7.1/.pc/spelling-errors.patch/TFBS/PatternGen/YMF.pm-133-# system 'ls -ltr';
##############################################
libtfbs-perl-0.7.1/.pc/spelling-errors.patch/TFBS/PatternGen/YMF.pm-146-# print STDERR "cd $dir;$command_line\n";
libtfbs-perl-0.7.1/.pc/spelling-errors.patch/TFBS/PatternGen/YMF.pm:147: my $resultstring = `cd $dir;$command_line`;
libtfbs-perl-0.7.1/.pc/spelling-errors.patch/TFBS/PatternGen/YMF.pm-148- # print STDERR $resultstring;
##############################################
libtfbs-perl-0.7.1/.pc/spelling-errors.patch/TFBS/PatternGen/YMF.pm-187- #print $command;
libtfbs-perl-0.7.1/.pc/spelling-errors.patch/TFBS/PatternGen/YMF.pm:188: `$command`;# or die "could not unlink $!";
libtfbs-perl-0.7.1/.pc/spelling-errors.patch/TFBS/PatternGen/YMF.pm-189-# return
##############################################
libtfbs-perl-0.7.1/.pc/spelling-errors.patch/TFBS/MatrixSet.pm-720- $args .= "$_ $args{$_} " for (keys(%args));
libtfbs-perl-0.7.1/.pc/spelling-errors.patch/TFBS/MatrixSet.pm:721: my @output = `$path/STAMP -ch $args -out $fh`;
libtfbs-perl-0.7.1/.pc/spelling-errors.patch/TFBS/MatrixSet.pm-722-