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

Hilmar Lapp hlapp at gmx.net
Sat Apr 7 17:13:24 EDT 2007

What I was suggesting was the indexer automatically does the  
reformatting, i.e., to have touch/change the input data if necessary  
(and obviously one would be able to turn this feature off when the  
correctness of the input formatting is known).

Are you suggesting that this automatic reformatting isn't possible?


On Apr 7, 2007, at 1:11 PM, Don Gilbert wrote:

> 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/

: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :

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