[Bioperl-l] Scoring an overlap

Chris Fields cjfields at uiuc.edu
Mon Sep 24 15:26:46 EDT 2007


I suppose if you can find a way to export the contig data into a  
Bio::SimpleAlign you look at the methods in  
Bio::Align::DNAStatistics.  SimpleAlign also has some builtin methods  
like average_percentage_identity, percentage_identity, etc, which may  
be worth a look.

chris

On Sep 24, 2007, at 2:07 PM, Florent Angly wrote:

> I see... Thanks for the replies Chad and Chris. Then I have two more
> questions!
> 1/ Do you know how to get a core dump that could help debug my
> segmentation fault? I have produced dumps of binary C programs before
> with gdb. I have used the Perl debugger for Perl scripts. But how to
> deal with C functions called by Perl?
> 2/ Is there an easier method to calculate an alignment score in  
> BioPerl
> than using Bio::Tools::dpAlign? I didn't seem to locate something  
> else,
> but who knows...
> I have workarounds for quantifying the quality of the overlap, so
> calculating a score is not critical for me (though I believe this  
> would
> be the most accurate/adapted method).
> Florent
>
> Chris Fields wrote:
>> As Chad mentioned it could be a stack issue, but it might be worth
>> filing a bug on.  I will note that bioperl-ext has seen very little
>> use in the last few years, so don't expect it to be fixed unless you
>> can contact the ext module author.
>>
>> chris
>>
>> On Sep 22, 2007, at 8:41 PM, Florent Angly wrote:
>>
>>> Eventually, I gave Bio::Tools::dpAlign a try. I had no luck  
>>> running it
>>> when installing its dependency, bioperl-ext v1.4 or v1.5.1.  
>>> However all
>>> the tests passed when installing the CVS version.
>>> So finally, here I am trying to score my alignments. For  
>>> alignments of 2
>>> small sequences, it works, but as soon as the sequences get  
>>> bigger than
>>> a few dozen nucleotides, it crashes:
>>> Segmentation fault (core dumped)
>>>
>>> I did not find any help in the documentation...
>>>
>>> Can I fix this? Is this a bug?
>>>
>>> Thanks for your help,
>>>
>>> Florent
>>>
>>> Florent Angly wrote:
>>>> Hi,
>>>> I need to quantify how good some overlaps in contigs are. I have
>>>> extracted the alignment of the overlapping region and only need to
>>>> score it. I noticed the Bio::Tools::dpAlign has a scoring function.
>>>> Is it the right tool for the right tool? Is there anything else?
>>>> Thank you,
>>>> Florent
>>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> Christopher Fields
>> Postdoctoral Researcher
>> Lab of Dr. Robert Switzer
>> Dept of Biochemistry
>> University of Illinois Urbana-Champaign
>>
>>
>>
>>
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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