[Biopython] Feature request: conservation line for fasta-m10 format

[Peter Cock]

On Fri, Apr 22, 2011 at 12:18 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> On Thu, Apr 21, 2011 at 10:47 PM, Aurelien Mazurie <ajmazurie at oenone.net> wrote:
>>
>>        Greetings,
>>        I used to write my own parser for FASTA alignment outputs, until
>> I realized Biopython had a dedicated module, Bio.AlignIO.FastaIO.
>> However I can't figure out how to get the conservation line out of the
>> FASTA results. ...
>
> ...
>
> Could you explain what you want to use it for? Part of the reason
> I'm asking is to better understand how you see it fitting the current
> object model.

By the way, which version of FASTA are you using? Older versions
didn't have the al_cons tag, but more importantly the new release
(probably all the FASTA 36.3.x releases) use the >>><<< line
differently and the Biopython parser needed to be updated.
If you use Biopython 1.57 with FASTA 36.3.4, you'll only see the
alignments for the first query sequence. Grab the latest code from
git if you need the fix (ask if you need clarification/help).

Peter