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.

  [email protected]                  - 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 [email protected]

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