[Bioperl-l] Recommended way to download qual files from Genbank?
cjfields at uiuc.edu
Fri Jan 11 12:09:40 EST 2008
I don't think this is possible with the current setup for
Bio::DB::GenBank (which the script uses). We'll have to investigate
whether it is possible to retrieve this data via NCBI's eutils; if so
we can try adding it in. If you want you can submit this as an
enhancement request via bugzilla for tracking:
On Jan 11, 2008, at 10:22 AM, Phillip San Miguel wrote:
> No problem getting sequence from genbank via a myriad of methods.
> But as the volume of non-finished sequence in genbank increases the
> importance of also obtaining quality values for a given sequence
> increases. Some records include quality values.
> I typically use bp_fetch.pl to grab a sequence from genbank:
> bp_fetch.pl -fmt fasta net::genbank:AC207960
> sends the fasta sequence to STDOUT. But that bp_fetch.pl wasn't
> designed to pull down quals evidently:
> bp_fetch.pl -fmt qual net::genbank:AC207960
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: You must pass a Bio::Seq::Quality or a Bio::Seq::PrimaryQual
> object to write_seq() as a parameter named "source"
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /usr/local/perl_5.8/lib/site_perl/
> STACK: Bio::SeqIO::qual::write_seq /usr/local/perl_5.8/lib/site_perl/
> STACK: /usr/local/perl/bin/bp_fetch.pl:313
> (running under bioperl 1.5.2)
> The quality values for this accession are in genbank as these URLs
> What is the best way to pull down these qual values? They aren't
> present in "GenBank(Full)" format. They are present in an ASN.1
> Advice would be appreciated.
> Purdue Genomics Core Facility
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> Bioperl-l at lists.open-bio.org
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Dept of Biochemistry
University of Illinois Urbana-Champaign
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