[Bioperl-l] Indexing qual files, Return of The Indexers

[Andy Nunberg]

I have been able to index .qual files by altering Bio::Index::Fasta.
Simple replace Fasta with qual in the _file_format method.

This tells SeqIO to return a qual object after it reads in the sequence...

I used the indexer to retreive specific qual files (and fasta files) for Phrap.
Unfortunately Phrap is picky about the format of the qual files and every
so often
gives a fatal error.  I have been attempting to contact the Phrap authors. 

Through all of this I noticed that write_seq method is not consistent among
the different
formats in SeqIO.
For example for fasta its write_seq($seqobj) or write_seq(@seqobj)
while for qual its write_seq(-source=>$seqobj)

This just may be a legacy issue..

Andy
*******************************************************************
Andy Nunberg, Ph.D
Computational Biologist
Orion Genomics, LLC 
(314) 615-6989
http://www.oriongenomics.com