===========================================================
.___ __ __
_________________ __ __ __| _/|__|/ |_
/ ___\_` __ \__ \ | | \/ __ | | \\_ __\
/ /_/ > | \// __ \| | / /_/ | | || |
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/_____/ \/ \/
grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-59-# Dumpvalue->new->dumpValue($seq);exit;
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl:60: my $geneid = safeval($seq, '{track-info}->[0]->{geneid}');
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-61- die "no geneid found!\n" unless $geneid; # this never happens, but doesn't hurt
##############################################
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-70- safeassign($llgene, 'symbol', $seq, '{gene}->[0]->{locus}'); # may be overwritten
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl:71: map { push(@{$llgene->{genenames}}, $_) } @{$seq->{gene}->[0]->{syn}} if(safeval($seq, '{gene}->[0]->{syn}'));
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-72- $llgene->{summary} = $seq->{summary} if($seq->{summary});
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl:73: $llgene->{chromosome} = $seq->{source}->[0]->{subtype}->[0]->{name} if(safeval($seq, '{source}->[0]->{subtype}->[0]->{subtype}') eq 'chromosome');
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-74- safeassign($llgene, 'chrmap', $seq, '{gene}->[0]->{maploc}');
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl:75: addxrefs($llgene, 'HGNC', $1) if(safeval($seq, '{gene}->[0]->{locus-tag}') =~ /HGNC:(\S+)/i);
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-76-
##############################################
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-83- # NOTE!!! species could be multiple species separated by ','
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl:84: my $id = safeval($seq, '{homology}->[0]->{source}->[0]->{src}->[0]->{tag}->[0]->{id}');
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl:85: my $species = safeval($seq, '{homology}->[0]->{heading}');
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-86- }
##############################################
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-101- {
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl:102: addxref($llgene, 'UNISTS', id => safeval($c, '{source}->[0]->{anchor}'),
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl:103: acc => safeval($c, '{source}->[0]->{src}->[0]->{tag}->[0]->{id}'));
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-104- }
##############################################
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-117- $acc = $product->{accession};
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl:118: $gi = safeval($product, '{source}->[0]->{src}->[0]->{tag}->[0]->{id}');
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-119- if($acc)
##############################################
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-134- {
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl:135: $trans->{assembly} = safeval($c, '{source}->[0]->{anchor}');
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-136- }
##############################################
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-139- {
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl:140: $trans->{variantcomment} = safeval($c, '{comment}->[0]->{text}');
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-141- }
##############################################
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-152- $acc = $p->{accession};
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl:153: $gi = safeval($p, '{source}->[0]->{src}->[0]->{tag}->[0]->{id}');
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-154- if($gi)
##############################################
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-180- my $dom;
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl:181: my $tmp = safeval($c2, '{comment}->[0]->{text}');
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-182- $dom->{score} = $tmp =~ /Blast Score: ([0-9.-]+)/;
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-183- ($dom->{start}, $dom->{end}) = $tmp =~ /Location: (\d+) - (\d+)/;
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl:184: $dom->{desc} = safeval($c2, '{source}->[0]->{anchor}');
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl:185: $dom->{xref} = { db => safeval($c2, '{source}->[0]->{src}->[0]->{db}'),
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl:186: ids => [{type=>'id',id=>safeval($c2, '{source}->[0]->{src}->[0]->{tag}->[0]->{id}')}]
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-187- };
##############################################
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-193- {
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl:194: $prot->{ccds} = safeval($c1, '{source}->[0]->{src}->[0]->{tag}->[0]->{str}');
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-195- }
##############################################
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-214- $acc = $product->{accession};
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl:215: $gi = safeval($product, '{source}->[0]->{src}->[0]->{tag}->[0]->{id}');
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-216- $ids{gi} = $gi if $gi;
##############################################
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-223- $acc = $product->{products}->[$j]->{accession};
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl:224: $gi = safeval($product->{products}->[$j], '{source}->[0]->{src}->[0]->{tag}->[0]->{id}');
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-225- $ids{'protgi' . ($j+1)} = $gi if $gi;
##############################################
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-237- {
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl:238: my $id = safeval($c, '{source}->[0]->{src}->[0]->{tag}->[0]->{str}');
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-239- if($id) # add xref to llgene
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-240- {
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl:241: my $db = uc(safeval($c, '{source}->[0]->{src}->[0]->{db}'));
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-242- next if $db =~ /\s+/ || $db =~ /HomoloGene/i; # homologene id here is not real id, and some of dblinks' DB name are not real DBs, we temporarily use space to identify those
##############################################
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-245- }
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl:246: my $url = safeval($c, '{source}->[0]->{url}');
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-247- if($url)
##############################################
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-249- $url =~ s/\s//g; # some urls have linebreaks in them
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl:250: my $desc = safeval($c, '{source}->[0]->{anchor}');
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-251- }
##############################################
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-260- {
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl:261: my $id = safeval($c, '{source}->[0]->{src}->[0]->{tag}->[0]->{str}');
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl:262: my $url = safeval($c, '{source}->[0]->{url}');
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-263- if($url)
##############################################
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-282- my $generif = $c->{text};
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl:283: my $pmid => safeval($c, "{refs}->[0]->{pmid}");
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-284- if($comment->{heading})
##############################################
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-287- my ($db, $id) = makexref($c);
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl:288: my $anchor = safeval($c, '{source}->[0]->{anchor}');
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-289- foreach my $c1 (@{$c->{comment}})
##############################################
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-294- }
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl:295: addxref($llgene, 'PUBMED', 'id' => safeval($c, "{refs}->[0]->{pmid}"));
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-296- }
##############################################
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-302- {
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl:303: my $detail = safeval($comment, '{comment}->[0]->{text}');
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl:304: if(safeval($comment, '{comment}->[0]->{source}'))
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-305- {
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl:306: my $db = safeval($comment, '{comment}->[0]->{source}->[0]->{src}->[0]->{db}');
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl:307: my $id = safeval($comment, '{comment}->[0]->{source}->[0]->{src}->[0]->{tag}->[0]->{id}');
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-308- }
##############################################
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-317- my $type = ($c->{text} =~ /related (.*)/)? $1 : $c->{text};
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl:318: my $anchor = safeval($c, '{source}->[0]->{anchor}');
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-319- my ($db, $id) = makexref($c);
##############################################
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-353- {
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl:354: my ($db, $id) = (safeval($c1, '{source}->[0]->{src}->[0]->{db}'),
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl:355: safeval($c1, '{source}->[0]->{src}->[0]->{tag}->[0]->{id}'));
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-356- addxref($llgene, $db, id => $id);
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-357- my $category = $map{uc($c->{label})};
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl:358: my $content = safeval($c1, '{source}->[0]->{anchor}');
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-359- }
##############################################
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-405- $ids{acc} = $p->{accession};
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl:406: my $gi = safeval($p, '{seqs}->[0]->{whole}->[0]->{gi}');
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-407- $ids{gi} = $gi if $gi;
##############################################
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-415- my $p1 = $p->{products}->[$j];
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl:416: $gi = safeval($p1, '{seqs}->[0]->{whole}->[0]->{gi}');
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-417- my ($gino, $accno) = ((($protgis{$gi})? $protgis{$gi} : 'protgi' . ($j+1)),
##############################################
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-427- $allseqs->{$p->{accession}}->{protein}->{$p1->{accession}}->{gi} = $ids{$gino} unless $allseqs->{$p->{accession}}->{protein}->{$p1->{accession}}->{gi}; # sometimes NCBI forgot to put refseq IDs into comments about Refseq sequences, e.g. Gene 616.
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl:428: if($p1->{comment} && safeval($p1, '{comment}->[0]->{type}') eq 'property' &&
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl:429: safeval($p1, '{comment}->[0]->{label}') eq 'EC')
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-430- {
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl:431: my $ec = safeval($p1, '{comment}->[0]->{text}');
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-432- # change dealing with EC number to add to xref
##############################################
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-444- $allseqs->{$p->{accession}}->{type} = $p->{type};
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl:445: my $tmp = safeval($p, '{genomic-coords}->[0]->{mix}->[0]->{int}') ||
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl:446: safeval($p, '{genomic-coords}->[0]->{int}');
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-447- $allseqs->{$p->{accession}}->{exons} = $tmp if($tmp);
##############################################
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-456- {
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl:457: my $tmp = safeval($p1, '{genomic-coords}->[0]->{packed-int}') ||
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl:458: safeval($p1, '{genomic-coords}->[0]->{int}');
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-459- if($tmp)
##############################################
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-469- addxref($llgene, 'REFSEQ', 'acc' => $l->{accession},
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl:470: 'gi' => safeval($l, '{seqs}->[0]->{int}->[0]->{id}->[0]->{gi}')); # trans and prots xrefs
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-471- }
##############################################
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-556- # tracking info about how this gene has changed
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl:557: if(safeval($seq, '{track-info}->[0]->{current-id}'))
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-558- {
##############################################
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-561- {
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl:562: my $tmpid = safeval($id, '{tag}->[0]->{id}');
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-563- push(@ids, "$id->{db}:$tmpid");
##############################################
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-576- my ($data, $key, $ds, $str) = @_;
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl:577: my $tmp = safeval($ds, $str);
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-578- $data->{$key} = $tmp if $tmp;
##############################################
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-626- my $c = shift;
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl:627: my $db = safeval($c, '{source}->[0]->{src}->[0]->{db}');
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl:628: my $id = safeval($c, '{source}->[0]->{src}->[0]->{tag}->[0]->{id}') ||
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl:629: safeval($c, '{source}->[0]->{src}->[0]->{tag}->[0]->{str}');
libbio-asn1-entrezgene-perl-1.730/examples/parse_entrez_gene_example.pl-630- # change the following as suited for your project