[Bioperl-l] FASTA format check

Dave Messina David.Messina at sbc.su.se
Thu May 22 05:24:31 EDT 2008


I don't think there's something like this in BioPerl (strangely -- I would
have thought Bio::SeqIO would have some validate() method. Perhaps if you
turn on debugging  or verbosity flags?). Someone who knows The Truth will
probably chime in here.

The Squid package that comes with HMMer <http://hmmer.janelia.org/> has a
program called seqstat. If you specify a file format (such as fasta) and
your file is not in that format, seqstat will complain (nicely).


Dave


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