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

[Florent Angly]

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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