From 0ce70064e461a2c852bf2377be31265f1dde4899 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Wed, 7 Mar 2007 15:49:54 +0000
Subject: [PATCH] Do RefSeq release info thing in RefSeqGPFFParser as well...
---
.../XrefParser/RefSeqGPFFParser.pm | 79 +++++++++++++------
1 file changed, 56 insertions(+), 23 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefParser/RefSeqGPFFParser.pm b/misc-scripts/xref_mapping/XrefParser/RefSeqGPFFParser.pm
index e5e13aad26..71dcfe510d 100644
--- a/misc-scripts/xref_mapping/XrefParser/RefSeqGPFFParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/RefSeqGPFFParser.pm
@@ -31,32 +31,65 @@ sub run {
my $source_id = shift;
my $species_id = shift;
my $file = shift;
+ my $release_file = shift;
if ($source_id < 1) {
- $source_id = XrefParser::BaseParser->get_source_id_for_filename(basename($file));
+ $source_id = $self->get_source_id_for_filename(basename($file));
}
if(!defined($species_id)){
- $species_id = XrefParser::BaseParser->get_species_id_for_filename($file);
+ $species_id = $self->get_species_id_for_filename($file);
}
- 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";
+ my $peptide_source_id =
+ $self->get_source_id_for_source_name('RefSeq_peptide');
+ my $dna_source_id =
+ $self->get_source_id_for_source_name('RefSeq_dna');
+
+ print "RefSeq_peptide source ID = $peptide_source_id\n";
+ print "RefSeq_dna source ID = $dna_source_id\n";
+
+ my $pred_peptide_source_id =
+ $self->get_source_id_for_source_name('RefSeq_peptide_predicted');
+ my $pred_dna_source_id =
+ $self->get_source_id_for_source_name('RefSeq_dna_predicted');
+
+ print "RefSeq_peptide_predicted source ID = "
+ . "$pred_peptide_source_id\n";
+ print "RefSeq_dna_predicted source ID = $pred_dna_source_id\n";
+
+ my $xrefs =
+ $self->create_xrefs( $peptide_source_id, $dna_source_id,
+ $pred_peptide_source_id, $pred_dna_source_id, $file,
+ $species_id );
+
+ if ( !defined($xrefs) ) {
+ return 1; #error
+ }
+ if ( !defined( $self->upload_xref_object_graphs($xrefs) ) ) {
+ return 1; # error
+ }
+
+ if ( defined $release_file ) {
+ # Parse and set release info.
+ my $release_io = $self->get_filehandle($release_file);
+ local $/ = "\n*";
+ my $release = $release_io->getline();
+ $release_io->close();
+
+ $release =~ s/\s{2,}/ /g;
+ $release =~ s/.*(NCBI Reference Sequence.*) Distribution.*/$1/s;
+ # Put a comma after the release number to make it more readable.
+ $release =~ s/Release (\d+)/Release $1,/;
+
+ print "RefSeq release: '$release'\n";
+
+ $self->set_release( $source_id, $release );
+ $self->set_release( $peptide_source_id, $release );
+ $self->set_release( $dna_source_id, $release );
+ $self->set_release( $pred_peptide_source_id, $release );
+ $self->set_release( $pred_dna_source_id, $release );
+ }
- my $pred_peptide_source_id = XrefParser::BaseParser->get_source_id_for_source_name('RefSeq_peptide_predicted');
- my $pred_dna_source_id = XrefParser::BaseParser->get_source_id_for_source_name('RefSeq_dna_predicted');
- print "RefSeq_peptide_predicted source ID = $pred_peptide_source_id; RefSeq_dna_predicted source ID = $pred_dna_source_id\n";
-
- my $xrefs =
- $self->create_xrefs( $peptide_source_id, $dna_source_id,
- $pred_peptide_source_id, $pred_dna_source_id, $file, $species_id );
-
- if(!defined($xrefs)){
- return 1; #error
- }
- if(!defined(XrefParser::BaseParser->upload_xref_object_graphs($xrefs))){
- return 1; # error
- }
return 0; # successful
}
@@ -73,12 +106,12 @@ sub create_xrefs {
my ( $peptide_source_id, $dna_source_id, $pred_peptide_source_id,
$pred_dna_source_id, $file, $species_id ) = @_;
- my %name2species_id = XrefParser::BaseParser->name2species_id();
+ my %name2species_id = $self->name2species_id();
- my %dependent_sources = XrefParser::BaseParser->get_dependent_xref_sources();
+ my %dependent_sources = $self->get_dependent_xref_sources();
-# my (%genemap) = %{XrefParser::BaseParser->get_valid_codes("mim_gene",$species_id)};
-# my (%morbidmap) = %{XrefParser::BaseParser->get_valid_codes("mim_morbid",$species_id)};
+# my (%genemap) = %{$self->get_valid_codes("mim_gene",$species_id)};
+# my (%morbidmap) = %{$self->get_valid_codes("mim_morbid",$species_id)};
my $refseq_io = $self->get_filehandle($file);
--
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