[Bioperl-l] LocatableSeq::subseq(): bug or not?

[Mark A. Jensen]

----- Original Message ----- 
From: "Chris Fields" <cjfields at illinois.edu>
To: "Mark A. Jensen" <maj at fortinbras.us>
Cc: "BioPerl List" <bioperl-l at lists.open-bio.org>
Sent: Tuesday, November 25, 2008 12:34 PM
Subject: Re: [Bioperl-l] LocatableSeq::subseq(): bug or not?


> Mark,
>
> Your subseq() patch appears to work just fine; no apparent tests are 
> failing, API doesn't change, so that will be added for the release. 
> We may need to define a new subseq()-like method to work properly 
> with  start/end coordinates that match only residues and are 
> consistent with  different coordinate systems (i.e. mapping), or we 
> can add that in as  a flag.

I'm willing to try my hand at this, if desired-- can you point me to 
the modules involved off the top of yer head?
MAJ

>
> Related to this, I have made a few commits defining groups of 
> symbols  for LocatableSeq ($GAP_SYMBOLS, $RESIDUE_SYMBOLS, 
> $FRAMESHIFT_SYMBOLS,  and the catchall $OTHER_SYMBOLS).  I had 
> already started down this  path anyway, so might as well finish it. 
> A remaining problem: they  are currently set as class global 
> variables, so there are some odd  scoping issues when using them 
> globally or locally (detailed in the  test suite as a TODO), and 
> they do not reset the $MATCHPATTERN.  I'll  set them up to be 
> object-scoped attributes in a future release.
>
> chris
>
> On Nov 24, 2008, at 8:04 AM, Mark A. Jensen wrote:
>
>> Bug #2682 contains a patch that modifies subseq() to strip gaps if 
>> desired. It also tries to fix the $replace weirdness.
>>
>> perldb transcript:
>> DB<11> $seq  = new Bio::PrimarySeq(-seq=>'--atg---gta--')
>>
>> DB<12> x $seq->subseq(1,3)
>> 0  '--a'
>> DB<13> x $seq->subseq(1,3,NOGAP)
>> 0  'a'
>> DB<15> x $seq->seq
>> 0  '--atg---gta--'
>> DB<16> x $seq->subseq(-START=>1, -END=>3, -REPLACE_WITH=>'tga')
>> 0  '--a'
>> DB<18> x $seq->seq
>> 0  'tgatg---gta--'
>> ## silly gap-stripper:
>> DB<21> x $seq->subseq(-START=>1, -END=>$seq->length,
>>                                         -REPLACE_WITH=>$seq->subseq(- 
>> START=>1,
>>                                                                     
>>                                -END =>$seq->length,
>>                                                                     
>>                                -NOGAP =>1))
>> 0  'tgatg---gta--'
>> DB<22> x $seq->seq
>> 0  'tgatggta'
>>
>> ----- Original Message ----- From: "Chris Fields" 
>> <cjfields at illinois.edu
>> >
>> To: "BioPerl List" <bioperl-l at lists.open-bio.org>
>> Sent: Sunday, November 23, 2008 7:31 PM
>> Subject: [Bioperl-l] LocatableSeq::subseq(): bug or not?
>>
>>
>>> Currently, we have Bio::LocatableSeq use the default 
>>> (Bio::PrimarySeq)  implementation of subseq().  However the 
>>> returned data apparently  clashes with the actual PrimarySeq 
>>> documentation:
>>>
>>> Function: returns the subseq from start to end, where the first 
>>> base
>>>           is 1 and the number is inclusive, ie 1-2 are the first 
>>> two
>>>           bases of the sequence
>>>
>>> So, should the following actually return the indicated range of 
>>> bases  (no gaps)?  Or should we clarify the above documentation to 
>>> indicate  subseq() returns the first x positions/columns 
>>> (anything)  instead of  'bases' (no gaps)?
>>>
>>> my $seq = Bio::LocatableSeq->new(
>>>   -seq => '--atg---gta--',
>>>   -strand => 1,
>>>   -start => 1,
>>>   -end => 6,
>>>   -alphabet => 'dna'
>>> );
>>>
>>> # comments indicate current returned val
>>> $seq->subseq(1,3);  # returns '--a'
>>> $seq->subseq(3,6);  # returns 'atg-'
>>> $seq->subseq(1,10); # returns '--atg---gt'
>>>
>>> chris
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>
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>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Marie-Claude Hofmann
> College of Veterinary Medicine
> University of Illinois Urbana-Champaign
>
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