[Biopython-dev] MAF Parser/Writer/Indexer

[Peter Cock]

On Mon, May 16, 2011 at 9:30 PM, Andrew Sczesnak wrote:
> On 05/16/2011 01:54 PM, Peter Cock wrote:
>>
>> That is my assumption for how dots have been used in alignment
>> formats.
>>
>> If you have some MAF examples using dots, that would be great.
>
> I added a snippet of mouse chromosome 10 from UCSC, but it doesn't have
> dots.  I've actually never come across one with dots.
>
> Added support for a 'track' line at the beginning of a file as well, among
> some other small changes.
>
> https://github.com/polyatail/biopython/commits/alignio-maf
>

Generally I'm happy, although after editing the BioPerl unit test,
perhaps we should rename it? And did you mean to alter the
newline at the end of the file?

https://github.com/polyatail/biopython/commit/d423d423cc87efeb8a27a9332927e42d1beacdf2

Also, could you rewrite this to avoid the use of handle.tell? Not all
handle objects support that (right?), and we shouldn't need it.

https://github.com/polyatail/biopython/commit/111cf69d7e435203a781f05f9f317bc9ced03560

Peter