[Biopython-dev] [Bug 2382] Generic Roche or GSFlex "FASTA" parser

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Thu Feb 19 18:48:46 UTC 2009


------- Comment #16 from biopython-bugzilla at maubp.freeserve.co.uk  2009-02-19 13:48 EST -------
(In reply to comment #15)
> Created an attachment (id=1247)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=1247&action=view) [details]
> command line tool/library for sifting through and transforming complex
> (multiline) records
> I should have posted this earlier. Basically this is the strategy I have been
> taking for dealing with complex record types (multiline), so that you can
> filter them the way you would with sed/awk or other stream editing tools. This
> is far from perfect, and it may not be helpful, but perhaps it will give a
> better idea of what I was picturing.

I just had a quick look, and in someways it reminds me of the Martel/Mindy
deprecated parsing infrastructure Biopython used to use.  This was very
flexible, perhaps too flexible as it had quite a learning curve - plus it
didn't scale well with large records.

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