[Bioperl-l] Scoring an overlap

Florent Angly florent.angly at gmail.com
Mon Sep 24 15:46:36 EDT 2007


Yes, right! That's the methods I use as my workarounds. =)
Thanks for suggesting.
Florent

Chris Fields wrote:
> 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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