From b96de5e2f866f6464cde53e98589a7077fdbe4d2 Mon Sep 17 00:00:00 2001
From: Bronwen Aken <ba1@sanger.ac.uk>
Date: Fri, 12 Oct 2007 14:53:08 +0000
Subject: [PATCH] Removed CDS parsing. Made pattern matching more strict when
choosing type (gene, transcript, translation) as 'pseudogene' transcripts had
previously been classified as genes.
---
.../XrefParser/Flybase_dmel_GFFv3_Parser.pm | 25 ++++++++++++++-----
1 file changed, 19 insertions(+), 6 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefParser/Flybase_dmel_GFFv3_Parser.pm b/misc-scripts/xref_mapping/XrefParser/Flybase_dmel_GFFv3_Parser.pm
index 10f0b1185b..be2de20e57 100644
--- a/misc-scripts/xref_mapping/XrefParser/Flybase_dmel_GFFv3_Parser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/Flybase_dmel_GFFv3_Parser.pm
@@ -6,7 +6,20 @@
# First of all, it read knows what all the gene, transcript and translation types are, found in column 3 of the gff file:
# Gene = gene
# Transcript = mRNA ncRNA snRNA tRNA rRNA pseudogene snoRNA miRNA
-# Translation = CDS protein
+# Translation = protein (could include CDS here but haven't ?)
+#
+# ID=FBgn => flybase_gene_id
+# ID=FBtr => flybase_transcript_id
+# ID=FBpp => flybase_polypeptide_id
+# Name=CG0123 => FlyBaseName_gene
+# Name=CG0123-RA => FlyBaseName_transcript
+# Name=CG0123-PA => FlyBaseName_translations
+# Dbxref=FlyBase:FBan => flybase_annotation_id
+# Dbxref=FlyBase_Annotation_IDs:CG0123 => gadfly_gene_cgid
+# Dbxref=FlyBase_Annotation_IDs:CG0123-RA => gadfly_transcript_cgid
+# Dbxref=FlyBase_Annotation_IDs:CG0123-PA => gadfly_translation_id
+# Alias= => flybase_synonym
+#
# For each line in the gff file for the above list of genes, transcript and translations, the following happens:
# The unique_id is read in from ID= (FBgn, FBtr, FBpp). This is the direct xref for all xrefs of this entry.
# An xref is made for the entry, using the ID as the xref's accession. Synonyms from Alias= are added to this xref.
@@ -57,7 +70,7 @@ sub new {
# my @gff_obj =qw( CDS exon gene mRNA ncRNA pseudogene rRNA snRNA snoRNA tRNA );
# this array may need to change between releases so check that it's updated
- my @gff_obj =qw( CDS gene mRNA ncRNA snRNA tRNA rRNA pseudogene snoRNA miRNA);
+ my @gff_obj =qw( gene mRNA ncRNA snRNA tRNA rRNA pseudogene snoRNA miRNA);
$self->gff_object_types(\@gff_obj);
#
@@ -129,7 +142,7 @@ sub new {
$self->source_name_prefix_modDDgene('modDD_gene'); # For Dbxref=modDD
my @gene_types = qw (gene) ;
- my @translation_types = qw (CDS protein);
+ my @translation_types = qw (protein);
# The transcript_types may change from release to release so check that this list is up-to-date
my @transcript_types = qw (mRNA ncRNA snRNA tRNA rRNA pseudogene snoRNA miRNA);
@@ -273,17 +286,17 @@ sub set_ensembl_object_type{
my ($self,$t) = @_ ; # $t is identifier in gff for object : CDS,mRNA,gene,pseudogene,snRNA,....
for my $hc (@{ $self->gene_types } ){
- if ($t=~m/$hc/){
+ if ($t=~m/^$hc$/){
return 'gene';
}
}
for my $hc (@{ $self->translation_types } ){
- if ($t=~m/$hc/){
+ if ($t=~m/^$hc$/){
return 'translation';
}
}
for my $hc (@{ $self->transcript_types} ){
- if ($t=~m/$hc/){
+ if ($t=~m/^$hc$/){
return 'transcript';
}
}
--
GitLab