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

[Chris Fields]

Never hurts to get started, just make sure that there is a note  
indicating the status of Bio::Assembly.  In fact, the discussion page  
for it might make a good sot for Bio::Assembly design.

chris
On Sep 19, 2009, at 9:20 PM, Florent Angly wrote:

> I suppose it is a good idea to wait until bioperl-live 1.6.1 is out  
> before doing any significant work on the sequence assembly module.
> Also, remember the assembly-related todo list: http://www.bioperl.org/wiki/Align_Refactor#Bio::Assembly-related
> 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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