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

Mark A. Jensen maj at fortinbras.us
Thu Mar 19 18:00:01 EDT 2009

Alexandr- I did write a patch for issue 2); I can make it available to you. It 
a proper insertion of a new seq at the specified $order, pushing the rest down
to make room. Not sure if the Core would like this committed?
cheers Mark
----- 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
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