From 1f2a64f873c857ec596365d942f24890165b50cf Mon Sep 17 00:00:00 2001
From: Glenn Proctor <gp1@sanger.ac.uk>
Date: Wed, 21 Sep 2005 13:49:08 +0000
Subject: [PATCH] Updated for new file format
>name|description
Now also loads xref descriptions
---
.../xref_mapping/XrefParser/AnophelesSymbolParser.pm | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefParser/AnophelesSymbolParser.pm b/misc-scripts/xref_mapping/XrefParser/AnophelesSymbolParser.pm
index a78fd8d089..0fec6fd2ee 100644
--- a/misc-scripts/xref_mapping/XrefParser/AnophelesSymbolParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/AnophelesSymbolParser.pm
@@ -10,7 +10,7 @@ use vars qw(@ISA);
# AnophelesSymbol database dump for anopheles - FASTA format
#
-# >ANXB10B,ANXB10B,ANXB10B,protein,Annexin B10B
+# >ANXB10B|Annexin B10B
# MSWYYTPHPTVVPAEDFDASADANALRKAMKGFGTDEQAIIDILCARSNGQRQEIAEAFKRELGRDLIDDLKSELGGKFEDVILGLMLRPEAYLCKQLHKAMDGIGTDEKSLIEII
# CPQTNDQIRAIVDCYEEMYSRPLAEHLCSETSGSFRRLLTMIIVGSRDPQGTVDPELAVEQAKQLYDAGEGKLGTDEEVFYKILAHASFDQLEIVFEEYKSLSGRTIEQALKAELS
# GELYDALSAIVECVQMAPHFFAKRLHKAMDGVGTDDATLIRIIVSRSEIDLQNIKDEFEQMYNKTLVSAVRSETSGDYKRALCALIGNA
@@ -34,7 +34,7 @@ sub run {
my ($header, $sequence) = $_ =~ /^>?(.+?)\n([^>]*)/s or warn("Can't parse FASTA entry: $_\n");
# deconstruct header - just use first part
- my ($accession, @rest) = split /,/, $header;
+ my ($accession, $description) = split /\|/, $header;
# make sequence into one long string
$sequence =~ s/\n//g;
@@ -42,6 +42,7 @@ sub run {
# build the xref object and store it
$xref->{ACCESSION} = $accession;
$xref->{LABEL} = $accession;
+ $xref->{DESCRITPION} = $description;
$xref->{SEQUENCE} = $sequence;
$xref->{SOURCE_ID} = $source_id;
$xref->{SPECIES_ID} = $species_id;
--
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