[Bioperl-l] issues with Bio::SimpleAlign add_seq function

Chris Fields cjfields at illinois.edu
Thu Mar 19 19:18:09 EDT 2009


ok, that's what I thought.

As for (1), if there is a discrepancy btwn how methods are using  
indices then this is a bug (odd that it didn't pop up before).  Could  
someone file this in bugzilla?

chris

On Mar 19, 2009, at 5:08 PM, Mark A. Jensen wrote:

> Hang on, looks like that change made it into the trunk: issue 2 is  
> resolved in the HEAD revision
> of Bio::SimpleAlign (http://code.open-bio.org/svnweb/index.cgi/bioperl/view/bioperl-live/trunk/Bio/SimpleAlign.pm 
> ).
> (revision 15533/cjfields)...
> ----- Original Message ----- From: "albezg" <albezg at gmail.com>
> To: <bioperl-l at bioperl.org>
> Sent: Thursday, March 19, 2009 5:30 PM
> Subject: [Bioperl-l] issues with Bio::SimpleAlign add_seq function
>
>
>> Hi all,
>> I'm using bioperl-1.6. Here are some things that bother me about
>> Bio::SimpleAlign add_seq function
>>
>> 1) Sequence order is counted from 0 not 1, unlike in other functions,
>> such as get_seq_by_pos and select.
>> 2) If position $order is already occupied then the old sequence is
>> removed. Is there a way to insert a new sequence in the middle of an
>> alignment?
>>
>> Alexandr
>> _______________________________________________
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>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
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