[Bioperl-l] a problem when using the Bioperl modules

[Jason Stajich]

Wei -

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 
> C.elegans.
> 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 
> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:368
> STACK: Bio::DB::Fasta::calculate_offsets 
> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Fasta.pm:770
> STACK: Bio::DB::Fasta::index_file 
> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Fasta.pm:680
> STACK: Bio::DB::Fasta::new 
> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Fasta.pm:491
> 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 
> well.
> thank you very very much.
> yours sincerely
> Wei Guifeng