[Bioperl-l] a problem when using the Bioperl modules
jason at bioperl.org
Mon Aug 23 11:56:47 EDT 2010
Please ask your questions on the bioperl mailing list, I cannot answer
questions directly for all requests.
Your problem has been answered by me on the list before so I urge you to
use the list archives as a starting point.
The line lengths of the fasta file sequence aren't the same length.
you need to run this
bp_sreformat -if fasta -of fasta -i ORIGINAL -o NEW
mv NEW ORIGINAL
or with sreformat
sreformat fasta ORIGINAL > NEW
mv NEW ORIGINAL
Guifeng Wei wrote, On 8/23/10 4:57 AM:
> Dear professor Stajich,
> So sorry to interrupt you. i came across a problem when i use the
> Bio::DB::Fasta modules of BioPerl. The aim i want to arrive at is to
> extract the subsequences accoording to the *.bed files which are the
> C.elegans genomic sequnece annotation. The code i programed is in the
> attached file.
> The genomic sequences file contains sequences from 6 chromosomes of
> when i run this program in the command line, the following error
> warnings was coming.
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: Each line of the fasta entry must be the same length except the last.
> Line above #301451 '
> ..' is 22 != 51 chars.
> STACK: Error::throw
> STACK: Bio::Root::Root::throw
> STACK: Bio::DB::Fasta::calculate_offsets
> STACK: Bio::DB::Fasta::index_file
> STACK: Bio::DB::Fasta::new
> STACK: bed_to_fasta.pl:14 <http://bed_to_fasta.pl:14>
> indexing was interrupted, so unlinking
> /home/wgf/WORM_DATA/elegans.WS190.dna.fa.index at
> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Fasta.pm line 1053.
> and therefore i write to you in hope that you can help me solve this
> problem,as well as, give me some suggestion about how to learn Bioperl
> thank you very very much.
> yours sincerely
> Wei Guifeng
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