[Biopython-dev] Biopython status

[Jared Flatow]

Hi all,

I've just started using Biopython and I am wondering about the status  
of the group, since I've heard rumors that its dying. So far I have  
found the library very useful, if not at times frustrating, though I  
will admit I am fairly new to developing python as well. I have been  
hesitant to make changes to existing code, however I have found that  
in a few cases it has been by far the best way to accomplish what I  
need, and have only done so in cases where it seems to be the *right*  
thing to do.

With that in mind, I have a few questions I was hoping you all could  
answer. First, how might I put these changes up for review in order  
to contribute back to the code base? The main changes have been to  
the AlignAce parser, since as it was it just ignored information  
contained in the alignace file regarding the motif instances (namely  
which input sequence they came from, where they started in the  
sequence, and what strand they were on). I have also needed to create  
a modified FASTA parser so that I can read things like quality score  
files. 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.

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.

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

Thanks!
Jared Flatow