From ed29fc7abb76f2306dbb29ac0994aaaf1a836fc9 Mon Sep 17 00:00:00 2001
From: Karyn Megy <kmegy@sanger.ac.uk>
Date: Fri, 17 Dec 2010 17:17:21 +0000
Subject: [PATCH] VectorBase Ribo.Prot.Gen DB parser
---
.../XrefParser/VBribosomalParser.pm | 81 +++++++++++++++++++
1 file changed, 81 insertions(+)
create mode 100644 misc-scripts/xref_mapping/XrefParser/VBribosomalParser.pm
diff --git a/misc-scripts/xref_mapping/XrefParser/VBribosomalParser.pm b/misc-scripts/xref_mapping/XrefParser/VBribosomalParser.pm
new file mode 100644
index 0000000000..19331b83e3
--- /dev/null
+++ b/misc-scripts/xref_mapping/XrefParser/VBribosomalParser.pm
@@ -0,0 +1,81 @@
+package XrefParser::VBribosomalParser;
+
+use strict;
+use POSIX qw(strftime);
+use File::Basename;
+use base qw( XrefParser::BaseParser );
+
+# Parse the external description file
+#
+# RPG_DB ID stable_id feature Name Description
+# MOS10001 AGAP011777 gene RpsA 40S ribosomal protein SA
+# MOS10002 AGAP003768 gene Rps2 40S ribosomal protein S2
+# MOS10003 AGAP001910 gene Rps3 40S ribosomal protein S3
+# ...
+
+if (!defined(caller())) {
+
+ if (scalar(@ARGV) != 1) {
+ print STDERR "\nUsage: VBribosomalParser.pm.pm file <source_id> <species_id>\n\n";
+ exit(1);
+ }
+
+ run($ARGV[0]);
+
+}
+
+sub run {
+
+ my $self = shift if (defined(caller(1)));
+
+ my $source_id = shift;
+ my $species_id = shift;
+ my $files = shift;
+ my $release_file = shift;
+ my $verbose = shift;
+
+ my $file = @{$files}[0];
+
+ print "source_id = $source_id, species= $species_id, file = $file\n" if($verbose);
+
+ if(!defined($source_id)){
+ $source_id = XrefParser::BaseParser->get_source_id_for_filename($file);
+ }
+ if(!defined($species_id)){
+ $species_id = XrefParser::BaseParser->get_species_id_for_filename($file);
+ }
+
+ my $added = 0;
+ my $count = 0;
+
+ my $file_io = $self->get_filehandle($file);
+
+ if ( !defined $file_io ) {
+ print STDERR "ERROR: Could not open file $file\n";
+ return 1;
+ }
+
+ while ( my $line = $file_io->getline() ) {
+ if ($line !~ /^#/) {
+ chomp $line;
+ my ($DB_id, $gene_id, $rien, $name, $description) = split("\t",$line); #and use the gene_id as accession
+ my $descr_full = "$DB_id - $description ($name)\n" ;
+
+ my $xref_id = $self->get_xref($gene_id,$source_id, $species_id);
+ if(!defined($xref_id)){
+ $xref_id = $self->add_xref($gene_id,"", $gene_id, $descr_full, $source_id, $species_id, "DIRECT");
+ $count++;
+ }
+ if(defined($gene_id) and $gene_id ne "-"){
+ $self->add_direct_xref($xref_id, $gene_id, "Gene", "") ;
+ $added++;
+ }
+ }
+
+ $file_io->close();
+
+ print "Added $count xrefs and $added Direct xrefs to genes for VBribosomal\n" if($verbose);
+ return 0;
+ }
+}
+1;
--
GitLab