[Bioperl-l] Is it possible to do contig alignments?

Sendu Bala bix at sendu.me.uk
Fri Aug 24 12:43:22 EDT 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 
> described.
[snip]
> 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.

Yes...


> 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.

http://www.bioperl.org/wiki/HOWTO:Writing_BioPerl_Tests


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