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

[Chris Fields]

Dan,

No, it hasn't made it in.  Currently, the problem is it doesn't have  
any tests attached, but that could be easily fixed if anyone wanted to  
donate a little time to getting them running.  My hands are a bit full  
with other stuff for the release.

We should have some ace files already to go in t/data somewhere if one  
were so inclined to do that, BTW  ;>

chris

On Sep 18, 2009, at 9:27 AM, Dan Bolser wrote:

> 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
>
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