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

Mark A. Jensen maj at fortinbras.us
Thu Mar 19 18:08:00 EDT 2009


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
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> 



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