[Bioperl-l] Bio::DB::Fasta check for ragged line widths

Don Gilbert gilbertd at cricket.bio.indiana.edu
Sat Apr 7 13:11:11 EDT 2007



Hilmar,

I have added reformatting where appropriate (in code that installs the 
files for indexing by Bio::DB::Fasta).  What I'm suggesting is a patch
to Bio::DB::Fasta to warn and die when the documented fixed width
that Bio::DB::Fasta requires isn't met.  I.e., keep other folks from
being bitten by this hard to identify requirement.  Then when they
see that this indexer is failing on inappropriate inputs, they also can reformat 
their Fasta to meet this requirement, and not continue to use the software with
bad results.  The operation of Bio::DB::Fasta is reading a sequence stream
and it doesn't touch/change the input data, so it would be hard to patch it
to re-format the input data.

- Don

-- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405
-- gilbertd at indiana.edu--http://marmot.bio.indiana.edu/


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