[Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl

[Dan Bolser]

2009/1/6 Chris Fields <cjfields at illinois.edu>:
> Could you archive the files and attach them to a bug report (you can mark it
> as an enhancement request).  We can take a look.
>
> http://bugzilla.open-bio.org/

Out of interest, has this been added? Where is it documented?

Cheers,
Dan.


> chris
>
> On Jan 6, 2009, at 5:13 PM, Joshua Udall wrote:
>
>> Chris et al. -
>>
>> A student and I have written code to do this - write ace files as well as
>> parse them one entry at a time.  In trying to use the Assembly::IO as it
>> was
>> in 1.5, we ran into problems with large ace files containing many entries
>> because of file handle limit issues with the inherited implementation
>> DB_File.  Our implementation simply reads one contig at a time instead of
>> first trying to slurp the whole ace into memory.  I'm happy to add it to
>> Bioperl, but I am not sure how to do it.  If I sent *.pm files to someone,
>> could they help me get it into bioperl?  It may not be perfect either, but
>> it should be a good start.
>>
>> Josh