[Bioperl-l] Fasta Qual files

Hilmar Lapp hlapp@gmx.net
Thu, 14 Sep 2000 10:07:51 +0200

"Brian A. Desany, Ph.D." wrote:
> This works great. My question is, does bioperl have the capability of
> treating fasta.qual files like this? I tried it on a fasta.qual file and it
> definitely did not work! Error message about unrecognized alphabet. It

I have code for reading Phred-produced seq/qual pairs of FASTA-formatted
files into Bio::QualSeq objects, which are merely Bio::Seq objects with
quality values (being truncated and reversed, too, when you
truncate/reverse the seq). The code can also write qual-files.

If you think this is useful for you I'll try to put it to the repository.


Hilmar Lapp                                email: hlapp@gmx.net
NFI Vienna, IFD/Bioinformatics             phone: +43 1 86634 631
A-1235 Vienna                                fax: +43 1 86634 727