[Bioperl-l] Recommended way to download qual files from Genbank?

Phillip San Miguel pmiguel at purdue.edu
Fri Jan 11 11:22:38 EST 2008


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

gives:

------------- 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/5.8.8/Bio/Root/Root.pm:359
STACK: Bio::SeqIO::qual::write_seq 
/usr/local/perl_5.8/lib/site_perl/5.8.8/Bio/SeqIO/qual.pm:205
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 
demonstrate:

http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=154937460

http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&list_uids=154937460&dopt=fasta

http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&list_uids=154937460&dopt=qual

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 format.

Advice would be appreciated.

-- 
Phillip
Purdue Genomics Core Facility






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