Bio::SearchIO::gmap_f9(3)

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://github.com/bioperl/bioperl-live/issues

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