From 8abf16e483b8f09637bbf247bac54129f8fc54c5 Mon Sep 17 00:00:00 2001
From: Arnaud Kerhornou <arnaud@ebi.ac.uk>
Date: Wed, 3 Oct 2012 14:26:33 +0000
Subject: [PATCH] PArser to import Phytozome xrefs for Glycine max
---
.../XrefParser/PhytozomeGmaxParser.pm | 92 +++++++++++++++++++
1 file changed, 92 insertions(+)
create mode 100644 misc-scripts/xref_mapping/XrefParser/PhytozomeGmaxParser.pm
diff --git a/misc-scripts/xref_mapping/XrefParser/PhytozomeGmaxParser.pm b/misc-scripts/xref_mapping/XrefParser/PhytozomeGmaxParser.pm
new file mode 100644
index 0000000000..e2a59886ea
--- /dev/null
+++ b/misc-scripts/xref_mapping/XrefParser/PhytozomeGmaxParser.pm
@@ -0,0 +1,92 @@
+package XrefParser::PhytozomeGmaxParser;
+
+use strict;
+use warnings;
+use Carp;
+use POSIX qw(strftime);
+use File::Basename;
+
+use base qw( XrefParser::BaseParser );
+
+# --------------------------------------------------------------------------------
+# Parse command line and run if being run directly
+
+sub run {
+
+ my ($self, $ref_arg) = @_;
+ my $source_id = $ref_arg->{source_id};
+ my $species_id = $ref_arg->{species_id};
+ my $files = $ref_arg->{files};
+ my $verbose = $ref_arg->{verbose};
+
+ if((!defined $source_id) or (!defined $species_id) or (!defined $files) ){
+ croak "Need to pass source_id, species_id and files as pairs";
+ }
+ $verbose |=0;
+
+ my $file = @{$files}[0];
+
+ my $gene_source_id = $self->get_source_id_for_source_name("PHYTOZOME_GMAX_GENE");
+
+ my $gmax_io = $self->get_filehandle($file);
+
+ if ( !defined $gmax_io ) {
+ print STDERR "ERROR: Could not open $file\n";
+ return 1; # 1 is an error
+ }
+
+ my $xref_count =0;
+ my $syn_count =0;
+
+ while ( $_ = $gmax_io->getline() ) {
+
+ chomp;
+
+ if ($_ =~ /^([^\t]+)\t[^\t]*\t[^\t]*\t[^\t]*\t[^\t]*\t[^\t]*\t[^\t]*\t[^\t]*\t([^\t]*)/) {
+ my ($gmax_id, $desc) = ($1,$2);
+
+ if ($verbose) {
+ #print STDERR "gmax_id, $gmax_id\n";
+ #print STDERR "desc: $desc\n";
+ }
+
+ my $locus_name = $gmax_id;
+ my $gene_xref_id = undef;
+
+ if ((defined $desc) && ($desc ne "")) {
+ $gene_xref_id = $self->add_xref({ acc => $gmax_id,
+ label => $locus_name,
+ desc => $desc,
+ source_id => $gene_source_id,
+ species_id => $species_id,
+ info_type => "DIRECT"} );
+ }
+ else {
+
+ # no description given
+
+ $gene_xref_id = $self->add_xref({ acc => $gmax_id,
+ label => $locus_name,
+ source_id => $gene_source_id,
+ species_id => $species_id,
+ info_type => "DIRECT"} );
+ }
+ $self->add_direct_xref($gene_xref_id, $gmax_id, "Gene", "DIRECT");
+
+ $xref_count++;
+
+ }
+ else {
+ if ($verbose) {
+ print STDERR "failed to parse line, $_\n\n";
+ }
+ }
+ }
+
+ $gmax_io->close();
+
+ print $xref_count." Phytozome_GMAX Xrefs added\n" if($verbose);
+ return 0; #successful
+}
+
+1;
--
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