[Bioperl-l] verify format
SMarkel at accelrys.com
Wed Jul 15 15:23:33 UTC 2009
for examples of how to read files using BioPerl. FASTA is one of the supported
Once you have a sequence object, e.g., after a line like
$seq_obj = $seqio_obj->next_seq;
you can use $seq_obj->alphabet to see if the sequence is "dna", "rna",
Note that this check is per sequence. There's no guarantee that all
sequences in a FASTA file are of a single type.
for other methods that can be called on a sequence object.
Scott Markel, Ph.D.
Principal Bioinformatics Architect email: smarkel at accelrys.com
Accelrys (SciTegic R&D) mobile: +1 858 205 3653
10188 Telesis Court, Suite 100 voice: +1 858 799 5603
San Diego, CA 92121 fax: +1 858 799 5222
USA web: http://www.accelrys.com
Vice President, Board of Directors:
International Society for Computational Biology
Co-chair: ISCB Publications Committee
Associate Editor: PLoS Computational Biology
Editorial Board: Briefings in Bioinformatics
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of tkd
> Sent: Wednesday, 15 July 2009 5:02 AM
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] verify format
> I'm computer scientist and I'm new in the bioinformatics world, and
> bioperl ...
> I have a small problem :
> I have a file, which has to be in FASTA format, but it could be wrong.
> So, I need :
> - to verify if my file is well-written in fasta format
> - to verify is the content of the fasta file is protein OR nucloetides
> I think there surely exists someting in bioperl to that but I didn't
> find anything.
> Thank for your help
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
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