[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


------------- 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 
STACK: Bio::SeqIO::qual::write_seq 
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 format.

Advice would be appreciated.

Purdue Genomics Core Facility

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