[Bioperl-l] fastq index

Chris Fields cjfields at illinois.edu
Wed Dec 29 22:34:32 EST 2010


May just wrap this for the indexer.  Thanks for the pointer Malcolm!

chris

On Dec 29, 2010, at 6:20 PM, Cook, Malcolm wrote:

> If you're looking for alternatives, I recommend: http://sourceforge.net/projects/cdbfasta/
> 
> No bioperl wrapper, but, hey, that's what `system` is for
> 
> Cheers,
> 
> Malcolm
> 
> 
> On 12/29/10 2:28 PM, "Chris Fields" <cjfields at illinois.edu> wrote:
> 
> On Dec 29, 2010, at 1:46 PM, Davis, Caleb F wrote:
> 
>> Hi all,
>> 
>> Retrieving fastq from an index with bio::index::fastq is not working for me. I try using the index creation and retrieval code as given here:
>> http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/Index/Fastq.html
>> using the fastq sequence given here:
>> http://www.bioperl.org/wiki/FASTQ_sequence_format
>> but I get this error:
>> ------------- EXCEPTION: Bio::Root::Exception -------------
>> MSG: NCYC361-11a03.q1k bases 1 to 1576 doesn't match fastq descriptor line type
>> STACK: Error::throw
>> STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:357
>> STACK: Bio::SeqIO::fastq::next_seq /usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO/fastq.pm:113
>> STACK: Bio::Index::AbstractSeq::fetch /usr/lib/perl5/site_perl/5.8.8/Bio/Index/AbstractSeq.pm:134
>> STACK: fetch_fastq_test.pl:11
>> 
>> The only other report of this behavior I could find is here:
>> http://permalink.gmane.org/gmane.comp.lang.perl.bio.general/17836
>> 
>> I get the same behavior when I use my own code and sequence. I hope I provided enough information. Sadly, I'm not sure what I'm doing wrong here.
>> 
>> --Caleb
> 
> Caleb,
> 
> Make sure you are using the latest BioPerl release via CPAN, or via github; the line number and error message don't correspond to the latest version.  If the problem persists, you may need to file a bug report for this with some example data and a script, or at least show some example data that is triggering the problem.
> 
> I believe the current indexing scheme used for FASTQ isn't up-to-date with the current parser (which underwent a complete refactoring a while back), so this would help tremendously, but it should be fairly easy to add proper indexing to this.  Jason and I briefly talked about FASTQ parsing a few months back in relation to speed of parsing, it could be much faster (my main concern initially was that it was correct).
> 
> chris
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