[Bioperl-l] Problems after changing display_id of a sequence in SimpleAlign

albezg albezg at gmail.com
Fri Mar 20 17:09:04 EDT 2009


Hi all,
I'm trying to change FASTA header(display_id) for a sequence in an
alignment(SimpleAlign).

There are no issues when I print it, however when I use AlignIO to write
the alignment to a FASTA file, it does not work. Is this behavior intended?

Demo code: http://github.com/jhannah/sandbox/tree/master/Bio_AlignIO_bug

The error:
------------- EXCEPTION -------------
MSG: No sequence with name [1/1-11]
STACK Bio::SimpleAlign::displayname
/scratch/BioSoftware/bioperl-live/Bio/SimpleAlign.pm:2659
STACK Bio::AlignIO::fasta::write_aln
/scratch/BioSoftware/bioperl-live/Bio/AlignIO/fasta.pm:200
STACK toplevel ./demo.pl:14
-------------------------------------

Alexandr


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