[Bioperl-l] Bio::SimpleAlign constructor?

Mark A. Jensen maj at fortinbras.us
Wed Jul 22 01:17:36 UTC 2009

Hi Paolo, 

I think I see what you want to do, however, it doesn't quite work
this way. I'm supposing you want to specify something like

s1/3-6 attc
s2/7-10 gaag

and obtain output like

s1 --attc----
s2 ------gaag

But (and this is why LocatableSeqs are "locatable"), the alignment 
described by the former data is always going to be

s1 attc
s2 gaag

so that I can query the alignment *column* number 1 and obtain
the residue coordinates of the original sequences in that column:

$loc = $aln->get_seq_by_pos(1)->location_from_column(1); # 3

or vice-versa

$col = $aln->column_from_residue_number( 's1', 3); # 1

As far as I know, you have to fill in the gaps yourself; a good
exercise, since you already have all the information you need, 
in having set up the start and end coordinates (which are really
the column coordinates in this model). 

If this wasn't what you had in mind, I apologize.

----- Original Message ----- 
From: "Paolo Pavan" <paolo.pavan at gmail.com>
To: <bioperl-l at lists.open-bio.org>
Sent: Thursday, July 16, 2009 6:17 AM
Subject: [Bioperl-l] Bio::SimpleAlign constructor?

> Hi,
> I have a brief question: I would like to know if there is a method to
> obtain a valid formatted and flush Bio::SimpleAlign object (i.e.
> properly filled with gaps on the right and on the left side of each
> sequence) given a bounch of Bio::LocatableSeq objects in which I have
> specified the -start and -end properties.
> Can anyone help me? Thank you very much,
> Paolo
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> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
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