From c4c3556a5315f3ee394af831c0719dd240a54ede Mon Sep 17 00:00:00 2001
From: James Allen <jallen@ebi.ac.uk>
Date: Thu, 1 Nov 2012 16:04:30 +0000
Subject: [PATCH] Strip newlines from gene descriptions
---
.../xref_mapping/XrefParser/FlybaseParser.pm | 60 ++++++++++---------
1 file changed, 31 insertions(+), 29 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefParser/FlybaseParser.pm b/misc-scripts/xref_mapping/XrefParser/FlybaseParser.pm
index 650ead8a75..e7959a70c5 100644
--- a/misc-scripts/xref_mapping/XrefParser/FlybaseParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/FlybaseParser.pm
@@ -13,14 +13,14 @@ my $verbose;
# The object types we'd like to parse.
our %object_types = ( gene => 1,
mRNA => 1,
- pre_miRNA => 1,
- miRNA => 1,
- ncRNA => 1,
protein => 1,
pseudogene => 1,
+ miRNA => 1,
+ ncRNA => 1,
+ pre_miRNA => 1,
rRNA => 1,
- snRNA => 1,
snoRNA => 1,
+ snRNA => 1,
tRNA => 1 );
# This is some statistics from the 5.4 file 'dmel-all-r5.4.gff.gz',
@@ -67,37 +67,36 @@ our %object_types = ( gene => 1,
# This hash will translate the Dbxref names in the data file into source
# names known by the Xref system.
-our %source_name_map = ( 'FlyBase' => 'flybase_annotation_id',
- 'GB' => 'EMBL',
- 'GB_protein' => 'protein_id',
- 'INTERPRO' => 'Interpro',
-# 'UniProt/Swiss-Prot' => 'Uniprot/SWISSPROT',
-# 'UniProt/TrEMBL' => 'Uniprot/SPTREMBL',
- 'bdgpinsituexpr' => 'BDGP_insitu_expr',
- 'dedb' => 'DEDb',
- 'flygrid' => 'FlyGrid',
- 'TF' => 'TransFac',
+# It's important to _not_ import the FlyBase UniProt annotations; they're
+# done at the gene level, which means that when we do our UniProt analysis
+# at the translation# level results are shifted to the gene level, which
+# messes up the web display.
+our %source_name_map = ( 'FlyBase' => 'flybase_annotation_id',
+ 'BIOGRID' => 'BioGRID',
'EPD' => 'EPD',
- 'MIR' => 'miRBase',
- 'MEROPS' => 'MEROPS',
- 'BIOGRID' => 'BioGRID',
- 'FlyReactome' => 'FlyReactome',
- 'GenomeRNAi_gene' => 'GenomeRNAi',
- 'INTERACTIVEFLY' => 'InteractiveFly',
- 'MITODROME' => 'MitoDrome',
- 'flyexpress' => 'FlyExpress',
- 'Rfam' => 'RFAM',
- #'FlyAtlas' => 'FlyAtlas',
- #'GCR' => 'GPCR',
- #'GLEANR' => 'GLEAN-R',
+ 'flyexpress' => 'FlyExpress',
+ 'FlyReactome' => 'FlyReactome',
+ 'GB' => 'EMBL',
+ 'GB_protein' => 'protein_id',
+ 'GenomeRNAi' => 'GenomeRNAi',
+ 'INTERACTIVEFLY' => 'InteractiveFly',
+ 'MEROPS' => 'MEROPS',
+ 'MIR' => 'miRBase',
+ 'MITODROME' => 'MitoDrome',
+ 'Rfam' => 'Rfam',
+ 'TF' => 'TransFac',
+ 'INTERPRO' => 'Interpro',
+ #'FlyAtlas' => 'FlyAtlas',
+ #'UniProt/Swiss-Prot' => 'Uniprot/SWISSPROT',
+ #'UniProt/TrEMBL' => 'Uniprot/SPTREMBL',
);
# This is for source_ids that depend on the type of 'ID' of the line.
our %special_source_name_map = (
'gene' => {
- 'Dbxref' => 'FlyBaseCGID_gene',
- 'Name' => 'FlyBaseName_gene',
- 'ID' => 'flybase_gene_id'
+ 'Dbxref' => 'FlyBaseCGID_gene',
+ 'Name' => 'FlyBaseName_gene',
+ 'ID' => 'flybase_gene_id'
},
'transcript' => {
'Dbxref' => 'FlyBaseCGID_transcript',
@@ -405,6 +404,9 @@ sub run {
# we have to put it back
$description =~ s/%2C/,/g;
+ # Embedded newlines wreak havoc further down the line
+ $description =~ s/[\n\r]//gm;
+
my $xref_id;
if ( exists( $xref_ids{$source_name}{$accession} ) ) {
--
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