From 0dc2e0946cf5191317841e8c277fe5ca8553c3d0 Mon Sep 17 00:00:00 2001
From: Glenn Proctor <gp1@sanger.ac.uk>
Date: Tue, 21 Dec 2004 13:32:38 +0000
Subject: [PATCH] Making mRNA xref dependent on peptide isn't needed and is
actually quite confusing on the web display.
---
.../XrefParser/RefSeqGPFFParser.pm | 60 +++++++++++--------
1 file changed, 35 insertions(+), 25 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefParser/RefSeqGPFFParser.pm b/misc-scripts/xref_mapping/XrefParser/RefSeqGPFFParser.pm
index 868b730c3a..49c2fd8792 100644
--- a/misc-scripts/xref_mapping/XrefParser/RefSeqGPFFParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/RefSeqGPFFParser.pm
@@ -41,7 +41,11 @@ sub run {
$species_id = XrefParser::BaseParser->get_species_id_for_filename($file);
}
- XrefParser::BaseParser->upload_xref_object_graphs(create_xrefs($source_id, $file, $species_id));
+ my $peptide_source_id = XrefParser::BaseParser->get_source_id_for_source_name('RefSeq_peptide');
+ my $dna_source_id = XrefParser::BaseParser->get_source_id_for_source_name('RefSeq_dna');
+ print "RefSeq_peptide source ID = $peptide_source_id; RefSeq_dna source ID = $dna_source_id\n";
+
+ XrefParser::BaseParser->upload_xref_object_graphs(create_xrefs($peptide_source_id, $dna_source_id, $file, $species_id));
}
@@ -54,7 +58,7 @@ sub run {
sub create_xrefs {
- my ($source_id, $file, $species_id) = @_;
+ my ($peptide_source_id, $dna_source_id, $file, $species_id) = @_;
my %name2species_id = XrefParser::BaseParser->name2species_id();
@@ -66,35 +70,39 @@ sub create_xrefs {
local $/ = "\/\/\n";
- my $type;
- if($file =~ /protein/){
+ my ($type, $source_id);
+ if ($file =~ /protein/) {
+
$type = 'peptide';
- }
- elsif($file =~ /rna/){
+ $source_id = $peptide_source_id;
+
+ } elsif ($file =~ /rna/) {
+
$type = 'dna';
- }
- else{
- die "Could not work out sequence type of sequences for $file\n";
+ $source_id = $dna_source_id;
+
+ } else{
+ die "Could not work out sequence type & source for $file\n";
}
while (<REFSEQ>) {
-
+
my $xref;
-
+
my $entry = $_;
chomp $entry;
-
+
my ($species) = $entry =~ /\s+ORGANISM\s+(.*)\n/;
$species = lc $species;
$species =~ s/^\s*//g;
$species =~ s/\s+/_/g;
$species =~ s/\n//g;
my $species_id_check = $name2species_id{$species};
-
+
# skip xrefs for species that aren't in the species table
if (defined ($species_id) and $species_id = $species_id_check) {
-
+
my ($acc) = $entry =~ /ACCESSION\s+(\S+)/;
my ($ver) = $entry =~ /VERSION\s+(\S+)/;
my ($description) = $entry =~ /DEFINITION\s+([^[]+)/s;
@@ -103,7 +111,7 @@ sub create_xrefs {
$description =~ s/\n//g;
$description =~ s/\s+/ /g;
$description = substr($description, 0, 255) if (length($description) > 255);
-
+
my ($seq) = $_ =~ /ORIGIN\s+(.+)/s; # /s allows . to match newline
my @seq_lines = split /\n/, $seq;
my $parsed_seq = "";
@@ -168,18 +176,20 @@ sub create_xrefs {
}
# Find associated mRNA
- my ($mrna) = $entry =~ /DBSOURCE\s+REFSEQ:\s+accession (.*)\n/;
+ #my ($mrna) = $entry =~ /DBSOURCE\s+REFSEQ:\s+accession (.*)\n/;
+ #
+ #if($mrna){
+ # my %mrna_dep;
+ # $mrna_dep{SOURCE_ID} = $source_id; # source is still RefSeq
+ # $mrna_dep{LINKAGE_SOURCE_ID} = $source_id;
+ # my ($mrna_acc,$mrna_ver) = split (/\./,$mrna);
+ #
+ # $mrna_dep{ACCESSION} = $mrna_acc;
+ # $mrna_dep{VERSION} = $mrna_ver;
+ # push @{$xref->{DEPENDENT_XREFS}}, \%mrna_dep;
+ #}
- if($mrna){
- my %mrna_dep;
- $mrna_dep{SOURCE_ID} = $source_id; # source is still RefSeq
- $mrna_dep{LINKAGE_SOURCE_ID} = $source_id;
- my ($mrna_acc,$mrna_ver) = split (/\./,$mrna);
- $mrna_dep{ACCESSION} = $mrna_acc;
- $mrna_dep{VERSION} = $mrna_ver;
- push @{$xref->{DEPENDENT_XREFS}}, \%mrna_dep;
- }
push @xrefs, $xref;
}# if defined species
--
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