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

Phillip San Miguel pmiguel at purdue.edu
Fri Jan 11 14:37:24 EST 2008


Hi Chris,
Thanks. I have submitted this as an enhancement request to bugzilla.
Phillip

Chris Fields wrote:
> 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:
>
> http://bugzilla.open-bio.org/
>
> chris
>
> 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
>>
>> 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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>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
>



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