[BioPython] Parsing the pairwise alignments from the FASTA tool

[Peter]

Hello everyone,

I'm currently interested in parsing the output from Bill Pearson's
FASTA tool in python, and would considering adding support for this to
Biopython.
See http://fasta.bioch.virginia.edu/fasta_www2/fasta_list2.shtml

Does anyone else on the list care about this file format?  If so, do
you have any python code you would like to share?  Otherwise, would
support for the "-m 10" output suffice?  This output is specifically
intended for parsing rather than being human readable.  There are
several different options for the output format, some of which looks a
bit like the BLAST plain text output.

Note that I do not mean the "typical" fasta format where each sequence
starts with a ">" line, which was originally introduced as an input
file format to the FASTA tools.  Biopython already deals with this
quite happily.

Peter

P.S. For anyone interested, BioPerl have had support for the human
readable FASTA output for a while, and judging from this thread, they
added support for the FASTA m10 variant last year:
http://bioperl.org/pipermail/bioperl-l/2007-April/025465.html