[Biopython-dev] Biopython status

[Peter]

Jared Flatow wrote:
> I have also needed to create a modified FASTA parser so that I can 
> read things like quality score files.

Could you be a little more specific - what exactly do you mean by a
quality score files (links and/or examples).  It may be that this
warrants setting up a new file format in Bio.SeqIO

> I would be happy to submit the changes to the group or an individual
>  for inspection, but I would like to avoid having to maintain my own
>  separate version of Biopython if possible.

As has already been said - please file some (enhancement) bugs and
attach your patches, or raise specific issues for discussion on this
mailing list.

Depending on the nature of your changes, you might be able to achieve
some of them by subclassing Biopython's objects - rather than literally
maintaining your own branch of the project.

> I am also wondering how it would be received if I did something like
>  add a to_fasta method to SeqRecord instead of having to go through 
> writing it to a file using a SeqIO when all I want is the string.

Out of interest, why do you want to create a FASTA record as a string?

Did you know you can write to a string using any Bio.SeqIO supported
file format using StringIO?  Perhaps we should spell this out more
explicitly in the documentation, but a motivating example would help.

I would suggest rather than adding a to_fasta method to the SeqRecord, 
simply write your own "seqrecord_to_string" function (or create a 
subclass of SeqRecord with this method).

> Finally, are there plans to move to a subversion repository at any 
> point?

It was raised a while ago, and our cunning plan was to let BioPerl try
the move first.  Once that has been proven, it should be fairly easy for
the OBF guys to also move us over.  I should email them to see how
things stand...

Peter