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

[Dan Bolser]

2009/9/20 Florent Angly <florent.angly at gmail.com>:

...

> Also, remember the assembly-related todo list:
> http://www.bioperl.org/wiki/Align_Refactor#Bio::Assembly-related

Thanks for that link Florent. It's great to see the wiki being put to
such good use in the context of OSS development! I need to make a
mental note - before posting, check the mailing list archives _and_
the wiki!

Cheers,
Dan.


> Florent
>
>
> Chris Fields wrote:
>>
>> Bug 2726
>>
>> http://bugzilla.open-bio.org/show_bug.cgi?id=2726
>>
>> chris
>>
>> On Sep 18, 2009, at 11:54 AM, Dan Bolser wrote:
>>
>>> 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
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>>
>>
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