[Bioperl-l] How to make a Bio::DB::SeqI from a Bio::SeqIO

Arnaud Mounier 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,
best regards,

« It occurs to me that our survival may depend upon our talking to one 
another. »
Dan Simmons.

Arnaud Mounier
INRA - UMR 1347 Agroecologie
CNRS - ERL 6300 IPM (Plant-Microorganism Interaction)
17, rue Sully - BP 86510 - F-21065 Dijon Cedex - France
Work phone : +33 380 693 167 - Fax : +33 380 693 753

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