[Bioperl-l] Bug in Contig.pm? How to compare two sequence objects?

Chris Fields cjfields at illinois.edu
Tue Jul 27 10:34:54 EDT 2010


On Jul 27, 2010, at 4:02 AM, Dan Bolser wrote:

> On 26 July 2010 18:54, Robson de Souza <robfsouza at gmail.com> wrote:
>> On Mon, Jul 26, 2010 at 12:37 PM, Dan Bolser <dan.bolser at gmail.com> wrote:
>>> Thanks again Robson,
>>> 
>>> One thing I was going to email the list about is a lack of tests for
>>> ace.pm and phrap.pm ... because of missing libs I'm not running the
>>> sam or the maq tests, so any changes that I'm making to Contig.pm /
>>> Scaffold.pm are not really being tested.
>>> 
>>> Do you think anyone on the list (or you) would be able to generate a
>>> few hundred tests to help me start modifying code with confidence?
>> 
>> I hope so. I was reading Chris's presentation at BOSC and he mentioned
>> that people are working on the support for the samtools so I believe
>> somebody must have a dataset they could share.
> 
> Bio::Assembly::IO::sam.pm is tested, but I don't run the tests because
> I don't have samtools installed. Also, (quick impression) method
> coverage is limited (Contig.pm has a lot of methods!).
> 
> I'll try to write some tests for ace.pm and phrap.pm.

Tests are good!

>> Never thought about it... but I can see that could be useful when
>> contigs are part of higher level assemblies, like scaffolds or
>> assembled chromosomes, but you could also achieve this by making
>> Contig.pm a Bio::RangeI or, perhaps better, a Bio::LocatableSeq. Any
>> reason to prefer the Bio::SeqFeatureI interface?
> 
> No. I don't have an overview of how the various objects relate to one
> another, so any choice is more or less arbitrary. I'll try to write a
> 'Sequence HOWTO'.
> 
> 
> Thanks again for help,
> Dan.

Dan, 

The current HOWTOs (Beginner's, Feature/Annotation) should have this information, along with the BioPerl tutorial.

chris




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