From 252da6c6b4502420e6dcfe843dc33b9d2b01f42b Mon Sep 17 00:00:00 2001
From: Abel Ureta-Vidal <abel@sanger.ac.uk>
Date: Tue, 12 Feb 2002 12:13:29 +0000
Subject: [PATCH] Adding database source and accession number in gene
description field
---
scripts/gene-descriptions.pl | 12 ++++++------
1 file changed, 6 insertions(+), 6 deletions(-)
diff --git a/scripts/gene-descriptions.pl b/scripts/gene-descriptions.pl
index 2caf8057a3..3e1fed1bd8 100755
--- a/scripts/gene-descriptions.pl
+++ b/scripts/gene-descriptions.pl
@@ -40,7 +40,7 @@ undef %gene_desc;
LINE:
while (<MAP>) {
chomp;
- ($ensp, $ensg, $db, $acc)=split(/\t/);
+ my ($ensp, $ensg, $db, $acc)=split(/\t/);
if ( defined($gene_desc{$ensg}) ) {
($prevdb, $prev_desc) = @{$gene_desc{$ensg}};
@@ -49,7 +49,7 @@ while (<MAP>) {
}
if ($db eq 'SWISS-PROT') {
$desc = $sp_desc{"$db:$acc"};
- $gene_desc{$ensg} = [ $db, $desc]; # kick out the SPTREMBL desc.
+ $gene_desc{$ensg} = [ $db, $desc, $acc ]; # kick out the SPTREMBL desc.
next LINE;
}
@@ -58,7 +58,7 @@ while (<MAP>) {
if ( &compare_desc($prev_desc, $desc) < 0 ) {
# new desc is better
# warn "new better: $desc (old was: $prev_desc)\n";
- $gene_desc{$ensg} = [ $db, $desc];
+ $gene_desc{$ensg} = [ $db, $desc, $acc ];
next LINE;
} else {
# warn "old better: $prev_desc (new is: $desc)\n";
@@ -68,13 +68,13 @@ while (<MAP>) {
}
} else {
$desc = $sp_desc{"$db:$acc"};
- $gene_desc{$ensg} = [ $db, $desc];
+ $gene_desc{$ensg} = [ $db, $desc, $acc ];
}
} # while <MAP>
# now dump the stuff to stdout.
foreach $ensg ( keys %gene_desc ) {
- ($db, $desc) = @{$gene_desc{$ensg}};
+ my ($db,$desc,$acc) = @{$gene_desc{$ensg}};
### final cleanup
### get rid of the Rik mess:
@@ -86,7 +86,7 @@ foreach $ensg ( keys %gene_desc ) {
s/^\s*\(\s*\)\s*$//g;
### add more as appropriate
- print STDOUT "$ensg\t$_\n" if $_; # =~ /[a-z]/;???
+ print STDOUT "$ensg\t $_ [Source:$db;Acc:$acc]\n" if $_; # =~ /[a-z]/;???
}
#### following taken from ensembl-external/scripts/family-input.pl
--
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