[Bioperl-l] seqDiff

Chris Fields cjfields at uiuc.edu
Fri Feb 2 15:33:46 EST 2007


Judging by the code you'll have to recreate the SeqDiff while  
iterating through various alleles; there is no method to remove  
particular variants or purge them (at least I couldn't find one).

I also noticed SeqDiff doesn't support deletions/insertions either;  
using a null allele (no seq) or leaving out either the mutant or  
original allele leads to errors.  I'll look into the latter, and I  
may try to add a method to at least purge variants and reset dna_mut().

chris

On Feb 2, 2007, at 4:06 AM, marian thieme wrote:

> HI,
>
> is there a way to put out all mutated sequences of a seqdiff object ?
> Suppose I add some variants via:
>
> $dnamut->add_Allele($a2);
> $dnamut->add_Allele($a3);
> $seqDiff->add_Variant($dnamut);
>
> and afterwards want to access the alternative sequences via
> $seqDiff->dna_mut()
>
> which allele is choosen when using dna_mut(), respective can I  
> control to access the first or the second alternate sequence ?
> If yes, how can I do this ?
>
> Regards,
> Marian
>
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>
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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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