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Gmane
From: Danyu Wu <danyuwu <at> hotmail.com>
Subject: can't get seq with bioperl
Newsgroups: gmane.comp.lang.perl.bio.general
Date: Wednesday 25th September 2013 22:07:24 UTC (over 3 years ago)
Hello,

I can not get the seq from a genbank format entry using bioperl when both
CONTIG and ORIGIN are present.  Any help is greatly appreciated!

An example:
LOCUS       YP_007988852            
          205 aa            linear   CON 22-MAY-2013

          DEFINITION  recombinase [Staphylococcus aureus].

          ACCESSION   YP_007988852

          VERSION     YP_007988852.1  GI:502045014

          ...

          CONTIG      join(WP_015639704.1:1..205)

          ORIGIN      

                  1 menrkfgyir vsskdqnegr qleamrkigi terdiyldkq
          sgknferany qllkriirkg

                 61 dilyihsldr fgrnkeeilq ewndltknie adivvldmpl
          ldttqykdsm gtfiadlvlq

                121 ilswmaeeer erirkrqreg idlalqngiq fgrspvvvsd
          efkevyrkwk akeltaveam

                181 qeagvkktsf yklvkahens ikvns

          //

      

My code is like:
$gb_bioperl = Bio::SeqIO->new(-file => "$Input_File", -format =>
"genbank");
$Entry_bioperl = $gb_bioperl->next_seq();
$seq = $Entry_bioperl->seq;

Could you please tell me how I can get the seq in this case?  Thanks a lot!

Danyu
 
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