[Bioperl-l] QRNA parser

[Jason Stajich]

I've added a parser for QRNA output on the main trunk Bio::Tools::QRNA.
This is of course experimental but may be useful to other people so I've
gone ahead and committed it.

The example files and a test in t/QRNA.t have been added as well as helper
script in scripts/utilities/search2alnblocks.PLS which is essentially a
rewrite of blast2qrna.pl from qrna-1.1.  I've only been testing on
qrna-1.2b so I don't know how it works on older versions.

A nice feature is automatic ability to remap locations from the alignment
space back into the orginal sequence coordinates if you provide your fasta
data formatted as ID/START-END (although gaps can still cause some
headaches here that I haven't fully debugged).

NAME
       Bio::Tools::QRNA - A Parser for qrna output

SYNOPSIS
         use Bio::Tools::QRNA;
         my $parser = new Bio::Tools::QRNA(-file => $qrnaoutput);
         while( my $feature = $parser->next_feature ) {

         }

DESCRIPTION
       Parses QRNA output (E.Rivas; http://www.genetics.wustl.edu/eddy/software/#qrna).

       This module is not complete, but currently it packs information from
       each QRNA alignment into a single Bio::SeqFeature::Generic object.

       Not all options for QRNA output have been tested or tried.  It has been
       tested on sliding window output (-w -x) and shuffled output (-b or -B).

       See t/QRNA.t for example usage.

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu