NAME

         GO::IO::Blast     - Gene Ontology Blast Reports DEPRECATED

SYNOPSIS

DESCRIPTION

       parses a blast report (must be a a blast that was performed on a seqdb that can with
       headers that can be mapped to go terms via the go database)

       takes the blast hits, and finds the corresponding GO terms (currently it requires the
       fasta to have "genename:" in header but we should make it configurable)

       using the GO terms, a GO::Model::Graph is built, with the blast hits attached according to
       product<->term links.

       Any blast hit H that corresponds to a term T implicitly corresponds to all the terms above
       T in the DAG; eg a hit to a G-protein coupled receptor is implicitly a hit to a
       transmembrane receptor.

       At every node, all the scores (including implicit scores from hits further down) are
       combined. Currently we are playing with this as the scording scheme:

       log2( 2 ** score1 + 2 ** score2 +.... 2** scoreN)

       Hits are only counted once at each node.

         TODO - use bioperl to parse full report if required
                  (currently parses summary)

         TODO - configurable ways to go from fasta header to GO terms

         TODO - different scoring schemes

         TODO - result object

PUBLIC METHODS - Blast

FEEDBACK

       Email cjm@fruitfly.berkeley.edu

       This library is free software; you can redistribute it and/or modify it under the same
       terms as Perl itself