[Biopython-dev] Proposal of a patch for FastaIO

[Roberto Mosca]

Dear Biopython developers,

I am new to this mailing list but I would like to propose a patch for
the parser of the fasta-m10 alignment format and I do not really know
how to do it...

The fact is that from a python script I need to access the details
(start and stop residues) of the alignment in every sequence and also
the E-value (sw_expect) which are saved in private variables (_al_start,
_al_stop and _annotations["sw_expect"]) but are not accessible from the
public interface of the SeqRecord and Alignment classes.

For this reason I had to modify the Bio/AlignIO/FastaIO.py file of my
local copy of BioPython.

Since I feel that other people could also benefit from these changes, I
would like to propose to include them in the standard distribution, but
I do not know what is the right procedure to follow. Could you help me?

I attach the patch file to FastaIO.py.

The code introduces two keys in the public "annotations" member of
SeqRecord ("start" and "end") and one key ("sw_expect") in the public
"annotations" member of Alignment.

Can someone give me any feedback on this?

I also have a github account (rmosca)...

Thank you in advance and thanks for this wonderful library that is
BioPython! 

Roberto

-- 
Roberto Mosca, Ph.D.

Structural Bioinformatics and Network Biology
Institute for Research in Biomedicine (IRB Barcelona)
Parc Científic de Barcelona
C/ Baldiri Reixac 10
08028 Barcelona - Spain

Email: roberto.mosca at irbbarcelona.org
Tel:   +34 93 40 39689
Web:   http://sbnb.irbbarcelona.org/people/roberto_mosca

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