[Bioperl-l] How to make a Bio::DB::SeqI from a Bio::SeqIO
arnaud.mounier at dijon.inra.fr
Fri Mar 9 07:42:16 EST 2012
Hi to everyone,
let's start to introduce myself : I'm a biological data mining engineer.
Formally I'm a computer scientist and I work in a biologist lab in
France. Kind of a rookie in biological computing.
My fist issue in this lab is to write a BioPerl script for TAIR
interrogations and I'm almost done but the final step is too high.
On one side there is 2 annotations files directly downloaded from TAIR
or get from the curator :
ATH_GO_GOSLIM.txt and gene_annotation.tair.
Handling the first file is the big issue for me (already told, rookie ;)
), I read it with a Bio::SeqIO object with the table format like this :
$TAIR_annotation_collection = Bio::SeqIO->new(
-file => $file,
-format => 'table',
-delim => "\t",
-display_id => 1,
-accession_number => 0,
-annotation_map => @mytags
where mytags looks like :
@mytags=qw(locusName tairAccession objectName relationType goTerm goID
tairKeywordId aspect goSlimTerm evidenceCode evidenceDescription
evidenceWith tairPublicationID annotator dateAnnotated);
the name of the 15 tags comes from the ATH_GO_README.txt
The field -accession_number is correctly read from the file.
So I have two questions :
- Is an array a correct the perl type for the annotation_map field ?
I can't find a complete description in my documentation.
- Once I have my Bio::SeqIO::Table handle the ATH_GO_GOSLIM.txt
correctly, I want to transform it in a Bio::DB:SeqI object. More
generally a BioPerl DB directly get from the Bio::SeqIO::Table object is
needed. The accession number has to be the index (I can't built a BioSQL
base). I can't find a suitable path to go throw this.
Have you any suggestions or links ?
Thank's for your help,
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