Alexey Morozov | 5 Oct 03:46 2013
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Re: can't get seq with bioperl

Could you please tell if $Entry_bioperl contains anything at all? Like,
Dumper it and see what's in there?

2013/9/26 Danyu Wu <danyuwu <at> hotmail.com>

>
>
>
> 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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> Bioperl-l <at> lists.open-bio.org
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>

--

-- 
Alexey Morozov,
LIN SB RAS, bioinformatics group.
Irkutsk, Russia.

Gmane