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

[Dan Bolser]

Please can you link to the bug that includes the code?


2009/9/18 Chris Fields <cjfields at illinois.edu>:
> 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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>
>