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

[Chris Fields]

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
>>>
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>>
>>