From e27dabf9cae2fbfb5824a4f93c42c68a3753cc24 Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Thu, 28 Jan 2010 09:50:50 +0000
Subject: [PATCH] Parser to add direct mapping fro swissprot entrys
---
.../XrefParser/UniProtDirectParser.pm | 141 ++++++++++++++++++
1 file changed, 141 insertions(+)
create mode 100644 misc-scripts/xref_mapping/XrefParser/UniProtDirectParser.pm
diff --git a/misc-scripts/xref_mapping/XrefParser/UniProtDirectParser.pm b/misc-scripts/xref_mapping/XrefParser/UniProtDirectParser.pm
new file mode 100644
index 0000000000..1dbd78a69f
--- /dev/null
+++ b/misc-scripts/xref_mapping/XrefParser/UniProtDirectParser.pm
@@ -0,0 +1,141 @@
+package XrefParser::UniProtDirectParser;
+
+use strict;
+
+use DBI;
+
+use base qw( XrefParser::BaseParser );
+
+# Parse file of Uniprot records and assign direct xrefs
+# All assumed to be linked to translation
+
+my $verbose;
+# --------------------------------------------------------------------------------
+# Parse command line and run if being run directly
+
+if (!defined(caller())) {
+
+ if (scalar(@ARGV) != 1) {
+ print "\nUsage: RefSeqParser.pm file.SPC <source_id> <species_id>\n\n";
+ exit(1);
+ }
+
+ run($ARGV[0], -1);
+
+}
+
+# --------------------------------------------------------------------------------
+
+sub run {
+
+ my $self = shift if (defined(caller(1)));
+
+ my $source_id = shift;
+ my $species_id = shift;
+ my $files = shift;
+ my $rel_file = shift;
+ $verbose = shift;
+
+ my %prefix = (9606 => "ENSP0", 10090 => "ENSMUSP0", 10116 => "ENSRNOP0");
+
+ if(!defined($prefix{$species_id})){
+ print "No prefix known for this species $species_id???\n";
+ return 1;
+ }
+
+ my $filename = @{$files}[0];
+
+ my $file_io = $self->get_filehandle($filename);
+ if ( !defined($file_io) ) {
+ return 1;
+ }
+
+ my $parsed_count = 0;
+
+
+ my %prot2ensembl;
+
+ my $count = 0;
+ while ( defined( my $line = $file_io->getline() ) ) {
+ my ($prot, $ens) = split /\s+/,$line;
+ if($ens =~ /$prefix{$species_id}/){
+ push @{$prot2ensembl{$prot}}, $ens;
+ }
+ }
+ my $dbi = XrefParser::BaseParser->dbi();
+
+ my $sw_source_id = XrefParser::BaseParser->get_source_id_for_source_name("uniprot/swissprot","sequence_mapped");
+ if($sw_source_id < 1){
+ die "Could not find source id for uniprot/swissprot ???\n";
+ }
+ else{
+ print "Source_id = $sw_source_id\n";
+ }
+ my $get_desc_sth = $dbi->prepare("select xref_id, version, label, description from xref where source_id = $sw_source_id and accession = ?");
+
+
+ my $get_dependents_sth = $dbi->prepare("select dependent_xref_id, linkage_annotation, linkage_source_id from dependent_xref where master_xref_id = ?");
+
+ my $add_dependent_xref_sth = $dbi->prepare("INSERT INTO dependent_xref (master_xref_id,dependent_xref_id,linkage_annotation, linkage_source_id) VALUES (?,?,?,?)");
+
+ my $err_count;
+ foreach my $key (keys %prot2ensembl){
+
+ #
+ # get the descrptions etc for the uniprot entry
+ #
+ $get_desc_sth->execute($key);
+ my ($old_xref_id, $version, $label, $description);
+ $get_desc_sth->bind_columns(\$old_xref_id, \$version, \$label, \$description);
+ $get_desc_sth->fetch;
+ if(!defined($old_xref_id)){
+ print STDERR "Could not find $key in the database\n" if ($err_count <10);
+ $err_count++;
+ next;
+ }
+ $count++;
+
+ #
+ # get the dependents
+ #
+ my %linkage_anotation=();
+ my %linkage_source_id=();
+ my ($dependent_xref_id, $linkage_annotation, $linkage_source_id);
+ $get_dependents_sth->execute($old_xref_id);
+ $get_dependents_sth->bind_columns(\$dependent_xref_id, \$linkage_annotation, \$linkage_source_id);
+ while($get_dependents_sth->fetch){
+ $linkage_anotation{$dependent_xref_id} = $linkage_annotation;
+ $linkage_source_id{$dependent_xref_id} = $linkage_source_id;
+ }
+
+
+# print $key."\t";
+ #
+ # Add the new xref
+ #
+
+ my $xref_id = XrefParser::BaseParser->add_xref($key, $version, $label, $description, $source_id, $species_id, "DIRECT");
+ foreach my $trans (@{$prot2ensembl{$key}}){
+ #
+ #add the direct xref entry
+ #
+
+ XrefParser::BaseParser->add_direct_xref( $xref_id, $trans, "Translation", '');
+# print ":".$trans;
+
+ #
+ #add the dependents
+ #
+ foreach my $dep (keys %linkage_anotation){
+ $add_dependent_xref_sth->execute($xref_id, $dep, $linkage_anotation{$dep}, $linkage_source_id{$dep});
+ }
+ }
+ }
+
+
+ print $count." entrys added\n".$err_count." not found\n";
+ return 0;
+}
+
+
+1;
--
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