[Bioperl-l] Problems with sort_alphabetically in Simple_align

[AUnderwood@PHLS.org.uk]

When trying to run the simplealign.pl script in the align folder of the
scripts I am having problems with the sort_alphabetically method. The script
as is will only print the msf format and then after the
$aln->sort_alphabetically(); command will not print out any of the pfam
alignments.

If I move the $aln->sort_alphabetically(); line to above the first print
statement then I get the following error:

MSG: No sequence at position [1]
STACK Bio::SimpleAlign::get_seq_by_pos
C:/Perl/site/lib/Bio/SimpleAlign.pm:587
STACK Bio::AlignIO::msf::write_aln C:/Perl/site/lib/Bio\AlignIO\msf.pm:180
STACK Bio::AlignIO::PRINT C:/Perl/site/lib/Bio/AlignIO.pm:502
STACK toplevel simplealign.pl:54

It appears that the $aln->sort_alphabetically(); command is removing entries
from the alignment rather than sorting them.

Does anyone have ideas on a fix


Many thanks


Anthony

Dr Anthony Underwood
Bioinformatics Unit
Central Public Health Laboratory
61 Colindale Avenue
London
NW9 5HT
t:    0208 2004400 ext. 3618
f:    0208 3583138
e: aunderwood@phls.org.uk