From bdb39ca185258cc2b18fc8e77cb7725bcc27992b Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Fri, 18 Feb 2005 18:01:01 +0000
Subject: [PATCH] redone to get all, not just first of each type of link to
interpro
---
.../xref_mapping/XrefParser/InterproParser.pm | 42 ++++++++-----------
1 file changed, 17 insertions(+), 25 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefParser/InterproParser.pm b/misc-scripts/xref_mapping/XrefParser/InterproParser.pm
index 5e5f5dffa3..afac2959e7 100644
--- a/misc-scripts/xref_mapping/XrefParser/InterproParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/InterproParser.pm
@@ -68,9 +68,7 @@ sub run {
# <db_xref protein_count="18" db="PFAM" dbkey="PF01278" name="Omptin" />
# <db_xref protein_count="344" db="TIGRFAMs" dbkey="TIGR00099" name="Cof-subfamily" />
- my $count = 0;
- my $count2 = 0;
- my $count3 = 0;
+ my %count;
local $/ = "</interpro>";
@@ -80,42 +78,36 @@ sub run {
my $interpro;
my $short_name;
- my $pfam;
- my $tigr;
my $name;
($interpro) = $_ =~ /interpro id\=\"(\S+)\"/;
($short_name) = $_ =~ /short_name\=\"(\S+)\"/;
($name) = $_ =~ /\<name\>(.*)\<\/name\>/;
- ($pfam) = $_ =~ /db\=\"PFAM\".*dbkey\=\"(\S+)\"/;
- ($tigr) = $_ =~ /db\=\"TIGRFAMs\".*dbkey\=\"(\S+)\"/;
-
-
+
if($interpro){
+# print $interpro."\n";
if(!get_xref($get_xref_sth, $interpro, $source_id)){
- $count++;
+ $count{INTERPRO}++;
$add_xref_sth->execute($interpro,'',$short_name, $name,$source_id,$species_id)
|| die "Problem adding ".$interpro."\n";
}
- if($pfam){
- if(!get_xref($get_interpro_sth, $interpro,$pfam)){
- $add_interpro_sth->execute($interpro,$pfam);
- $count2++;
- }
- }
- if($tigr){
- if(!get_xref($get_interpro_sth, $interpro,$tigr)){
- $add_interpro_sth->execute($interpro,$tigr);
- $count3++;
+
+ while( /db="(PROSITE|PFAM|PRINTS|PREFILE|PROFILE|TIGRFAMs)"\s+dbkey="(\S+)"/cgm ) {
+ my ( $db_type, $id ) = ( $1, $2 );
+# print $db_type."\t".$id."\n";
+ if(!get_xref($get_interpro_sth, $interpro,$id)){
+ $add_interpro_sth->execute($interpro,$id);
+ $count{$db_type}++;
}
- }
+ }
}
}
+
close (LONG);
-
- print "\t$count xref successfully loaded.\n";
- print "\t$count2 interpro/pfam relationships added\n";
- print "\t$count3 interpro/tigr relationships added\n";
+# die "\n";
+ for my $db ( keys %count ) {
+ print "\t".$count{$db}." $db loaded.\n";
+ }
}
--
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