[Biopython-dev] [Bug 2382] Generic FASTA parser

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2382





------- Comment #2 from biopython-bugzilla at maubp.freeserve.co.uk  2007-10-16 17:02 EST -------
Are there any other "FASTA like" formats you know of, in addition to
traditional sequence data and the 454 GSFlex quality score files?

We could do this using the old Scanner/Consumer model (see the pre-Martel
parse, CVS revision 1.8 of Bio/Fasta/__init__.py for example).

http://cvs.biopython.org/cgi-bin/viewcvs/viewcvs.cgi/biopython/Bio/Fasta/__init__.py?rev=1.8&cvsroot=biopython&content-type=text/vnd.viewcvs-markup

The scanner would be the same for all formats, and would pass the data with
whitespace (spaces, new lines etc) as is.  We could then have one consumer for
each supported FASTA variant:

_Scanner           Scans a FASTA-format stream.
_RecordConsumer    Consumes FASTA data to a Record object.
_SequenceConsumer  Consumes FASTA data to a Sequence object.
_QualityConsumer   (new) could build a list of integers for each record?


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