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Gmane
From: =?ISO-8859-1?Q?T=E9letch=E9a_St=E9phane?= <stephane.teletchea <at> inserm.fr>
Subject: Problem using column_from_residue_number
Newsgroups: gmane.comp.lang.perl.bio.general
Date: Tuesday 23rd April 2013 16:10:23 UTC (over 3 years ago)
Dear bioperlers,

I am facing a problem I used to encounter in the past and failed to 
report it properly.

I am either mis-using it or there is a bug, I would like your feedback.

Consider the alignment between sequence A and B in test.ali,
and the bioperl_test.pl as examples (attached to this mail).

I would like to know at position i what is the amino acid of seq A,
and what is the amino acid in position i in sequence B (of course these 
residues may not be aligned).

The problem is:

a) I cannot parse the first residue of the alignment, it has to start at 
1, otherwise I have:

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Second argument residue number missing
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:472
STACK: Bio::SimpleAlign::column_from_residue_number 
/usr/share/perl5/Bio/SimpleAlign.pm:2626
STACK: ./bioperl_test.pl:19
-----------------------------------------------------------

b) Although, if I understand correctly, this function should return only 
the residues,
sometimes I have a gap inserted, so the function is not working properly:

./bioperl_test.pl |grep '-'
P:11 for seq 1 and -:30 for seq 2
S:76 for seq 1 and -:96 for seq 2
-:124 for seq 1 and L:146 for seq 2
-:150 for seq 1 and K:170 for seq 2
-:175 for seq 1 and I:190 for seq 2
-:202 for seq 1 and L:215 for seq 2
-:224 for seq 1 and G:233 for seq 2
W:264 for seq 1 and -:263 for seq 2
S:296 for seq 1 and -:297 for seq 2
-:343 for seq 1 and S:345 for seq 2
-:369 for seq 1 and H:361 for seq 2

Can we discuss it here or I have to open a bug report?

Thanks in advance,

Stéphane

-- 
Equipe DSIMB - Dynamique des Structures et
des Interactions des Macromolécules Biologiques
INTS, INSERM-Paris-Diderot UMR-S665
6 rue Alexandre Cabanel - 75739 Paris cedex 15- France
Tél : +33 144 493 057
Fax : +33 147 347 431
http://www.dsimb.inserm.fr / http://steletch.free.fr
 
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