[Bioperl-l] fastq index

Davis, Caleb F cdavis at bcm.edu
Wed Dec 29 14:46:14 EST 2010


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




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