[Bioperl-l] parsing 'parsed blast data'

[Wiepert, Mathieu]

Hi,

I am sure there is a way, but you could just rip the code out of the modules that parse the description header ;-)  Might work faster?  (Like that hasn't occurred to you already of course!)  Or, treat them like fasta streams to Bio::SeqIO seq objects that have no sequence, and then ask for info from the seq objects?  Not sure if you can do that, or want to...

-mat

> -----Original Message-----
> From: Charles Hauser [mailto:chauser@duke.edu]
> Sent: Monday, December 02, 2002 11:25 AM
> To: BioPerl-List
> Subject: [Bioperl-l] parsing 'parsed blast data'
> 
> 
> All,
> 
> I have a lot of parsed tab-delimited blast data from which I 
> would like
> to extract 'accession' and 'description' from the 'subj_name' 
> field ala
> $hit->accession(), $hit->description.  The data were generated from
> blastx vs nr. 
> 
> It would be really nice if I could trick Bio:SearchIO into 
> thinking this
> was a blast report and extract the data that way - possible?
> 
> 
> Sample data field: 
> 
> pir||T43266 DNA-directed DNA polymerase (EC 2.7.7.7) delta chain -
> fission yeast (Schizosaccharomyces pombe) gb|AAA35303.1| (L07734) DNA
> polymerase delta [Schizosaccharomyces pombe] 
> 
> Charles
> 
> 
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