Provided by: libbio-perl-perl_1.6.901-2_all bug

NAME

       Bio::SearchIO::gmap_f9 - Event generator for parsing gmap reports (Z format)

SYNOPSIS

          # Do not use this object directly - it is used as part of the
          # Bio::SearchIO system.

           use Bio::SearchIO;
           my $searchio = Bio::SearchIO->new(-format => 'gmap',
                                             -file   => 't/data/her2.gmapz');
           while( my $result = $searchio->next_result ) {
               while( my $hit = $result->next_hit ) {
                   while( my $hsp = $hit->next_hsp ) {
                       # ...
                   }
               }
           }

DESCRIPTION

       This object encapsulated the necessary methods for generating events suitable for building
       Bio::Search objects from a GMAP "compressed" report (from gmap run with -Z flag) Read the
       Bio::SearchIO for more information about how to use this.

   REVERSE STRAND AND BIOPERL COORDINATES
       I believe that I'm doing the correct thing when reporting hits on the negative strand of
       the genome.  In particular, I've compared the "exons" this code generates with the set
       returned by ncbi's megablast web service.  NCBI's hsp's are ordered differently and have a
       different genomic location (off by ~18,000,000 bases, padding?) but the starts, ends, and
       lengths were similar and my strand handling matches theirs.  E.g.

          CDNA                            GENOME
        start  end    strand   start           end             strand

       blast
         1913    2989 1    86236731  86237808  -1
         1  475  1    86260509  86260983  -1
         1510    1727 1    86240259  86240476  -1
         841     989  1    86243034  86243182  -1
         1381    1514 1    86240630  86240763  -1
         989     1122 1    86242457  86242590  -1
         599     729  1    86247470  86247600  -1
         473     608  1    86259972  86260107  -1
         1255    1382 1    86240837  86240964  -1
         730     842  1    86244040  86244152  -1
         1813    1921 1    86238123  86238231  -1
         1725    1814 1    86239747  86239836  -1
         1167    1256 1    86241294  86241383  -1
         1120    1188 1    86242319  86242387  -1

       gmap
         1  475  1    104330509 104330983 -1
         476     600  1    104329980 104330104 -1
         601     729  1    104317470 104317598 -1
         730     841  1    104314041 104314152 -1
         842     989  1    104313034 104313181 -1
         990     1121 1    104312458 104312589 -1
         1122    1187 1    104312320 104312385 -1
         1188    1256 1    104311294 104311362 -1
         1257    1382 1    104310837 104310962 -1
         1383    1511 1    104310633 104310761 -1
         1512    1726 1    104310260 104310474 -1
         1727    1814 1    104309747 104309834 -1
         1815    1917 1    104308127 104308229 -1
         1918    2989 1    104306731 104307802 -1

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send
       your comments and suggestions preferably to the Bioperl mailing list.  Your participation
       is much appreciated.

         bioperl-l@bioperl.org                  - General discussion
         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their
       resolution. Bug reports can be submitted via the web:

         https://redmine.open-bio.org/projects/bioperl/

AUTHOR - George Hartzell

       Email hartzell@alerce.com

CONTRIBUTORS

       Additional contributors names and emails here

APPENDIX

       The rest of the documentation details each of the object methods.  Internal methods are
       usually preceded with an underscore (_).

   next_result
        Title   : next_result
        Usage   : $result = stream->next_result
        Function: Reads the next ResultI object from the stream and returns it.
        Returns : A Bio::Search::Result::ResultI object
        Args    : n/a