[Biopython-dev] Biopython status

[Michiel De Hoon]

Hi Jared,

> I've just started using Biopython and I am wondering about the status  
> of the group, since I've heard rumors that its dying.

>From looking at the activity on the Biopython mailing lists in recent months,
it doesn't seem to be 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.

One thing to keep in mind is that Biopython started about eight years ago,
and some approaches that seemed to be a good idea at that time may not seem
to be so now. Nevertheless, I feel that Biopython is moving in the right
direction in terms of ease-of-use.

> 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).

In this case, it is a good idea to contact the current maintainer of
Bio.AlignAce, either via the mailing list or directly. From the Biopython
CVS, it seems that Bartek is currently the main maintainer of Bio.AlignAce,
so it would be a good idea to discuss with him.

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

At some point, Biopython had several (two or three?) Fasta parsers, two Fasta
formats, etc. This is a situation we should definitely avoid. So if your
modifications fit in well with the existing Fasta parser in Bio.SeqIO, it may
very well be accepted into Biopython. Otherwise, it's better to leave it out.
This is just my opinion though.

> 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.

This sounds like feature creep to me, so I would be against it. It's easy to
add code to Biopython, it's much harder to remove stuff. Code bloat is a real
problem in Biopython.

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

There were some plans at some point, but I don't know the current status.

Best,

--Michiel.


Michiel de Hoon
Center for Computational Biology and Bioinformatics
Columbia University
1150 St Nicholas Avenue
New York, NY 10032



-----Original Message-----
From: biopython-dev-bounces at lists.open-bio.org on behalf of Jared Flatow
Sent: Mon 10/15/2007 8:08 PM
To: biopython-dev at lists.open-bio.org
Subject: [Biopython-dev] Biopython status
 
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
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