[Bioperl-l] Scoring an overlap
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.
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
> 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
> than using Bio::Tools::dpAlign? I didn't seem to locate something
> 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
> be the most accurate/adapted method).
> 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.
>> 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 Angly wrote:
>>>> 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,
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>> Christopher Fields
>> Postdoctoral Researcher
>> Lab of Dr. Robert Switzer
>> Dept of Biochemistry
>> University of Illinois Urbana-Champaign
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Lab of Dr. Robert Switzer
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