[Bioperl-l] Extract sequences of CDS regions from Genbank formatted file

[Ashton Trey Belew]

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  Hello Cacau,
  Attached is a script I use for exactly this purpose.  It also makes
a gff and some other stuff which might be of interest.

  It makes use of Getopt::Long and assumes you will feed it --input or
- -i followed by the genbank file.  If you forget (as I often do), it
will ask you for the genbank filename.
  If you provide -o or --output, that will be the basename of the
following output files:

  1.  A gff of all entries
  2.  A gff of all the gene entries
  3.  A gff of CDS entries
  4.  A gff of the inter-cds regions
  5.  A fasta file of all the coding sequences
  6.  A fasta file of the coding sequences as peptide sequence.

 Good luck,
 -Trey

On 08/12/2014 03:10 PM, Cacau Centurion wrote:
> Hi all,
> 
> I was wondering if there is a way to directly extract all sequences
> of CDS regions from a Genbank formatted file using bioperl?
> 
> Yours, Cacau
> 
> 
> _______________________________________________ Bioperl-l mailing
> list Bioperl-l at mailman.open-bio.org 
> http://mailman.open-bio.org/mailman/listinfo/bioperl-l
> 
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