[Bioperl-l] Check sequence format, question
cjfields at uiuc.edu
Wed Nov 1 23:28:11 EST 2006
On Nov 1, 2006, at 6:15 PM, Eugene Bolotin wrote:
> Dear bioperl mailing list,
> I trying to get sequence from a file using Bio::SeqIO, before I do
> I want to make sure that the file is in a correct Fasta sequence
> format. I
> want it to spit out an error message if it is in any other format.
> What is the easiest way to do it?
> Eugene Bolotin
> Sladek Lab.
There is no formal FASTA definition that is universally accepted
beyond having the first line start with '>' and an optional
description, with the sequence in subsequent lines.
Bio::SeqIO isn't currently set up to validate sequence formats
directly, but you could try preparsing the data using
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign
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