[Bioperl-l] Is it possible to do contig alignments?
bix at sendu.me.uk
Fri Aug 24 16:43:22 UTC 2007
Florent Angly wrote:
> Thanks for all the replies.
> Sendu Bala wrote:
>> Isn't Bio::Assembly::Contig what you need?
> I'm using this module already to manipulate the contigs, but there's
> no option that I know of to _display_ the contigs in the way I
> I think the best way to provide an out-of-the-box solution for
> displaying contigs the described way would be to _not_ use Bio::Align
> at all, but rather to create a new assembly IO module like
> Bio::Assembly::IO::simpleout for example. That would be useful.
> The reason I wanted to visualize these contigs is because I made a
> Bio::Assembly::IO module for TIGR Assembler files that I intend on
> submitting to BioPerl.
That's wonderful... might I cheekily suggest that the solution to your
problem is to extend your IO module so that it does the 'O' as well? Ie.
unlike the other IO modules, write_assembly() is actually implemented.
Then you can round-trip to ensure your next_assembly() method has no bugs.
> I've read the documentation on the Wiki so if a BioPerl developer
> would please like lo step up and contact me directly for checking my
> code, that would be nice =)
If no one does, post it as an enhancement request to bugzilla. A test
script is a must.
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