Login or Register to Ask a Question and Join Our Community

Linux and UNIX Man Pages

Linux & Unix Commands - Search Man Pages

bio::searchio::gmap_f9(3pm) [debian man page]

Bio::SearchIO::gmap_f9(3pm)				User Contributed Perl Documentation			       Bio::SearchIO::gmap_f9(3pm)

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

perl v5.14.2							    2012-03-02					       Bio::SearchIO::gmap_f9(3pm)

Check Out this Related Man Page

Bio::SearchIO::cross_match(3pm) 			User Contributed Perl Documentation			   Bio::SearchIO::cross_match(3pm)

NAME

       Bio::SearchIO::cross_match - CrossMatch-specific subclass of Bio::SearchIO

SYNOPSIS

	   # Working with iterations (CrossMatch results)
	   my $searchIO = Bio::SearchIO->new( -format => 'cross_match',
				   -file   => "$file.screen.out" )
	   while(my $r = $searchIO->next_result) {
	     while(my $hit = $r->next_hit) {
	       while(my $hsp = $hit->next_hsp) {
		  #Do the processing here.
	       }
	     }
	   }
       # See Bio::SearchIO for information about working with Results.

       # See Bio::SearchIO # for details about working with Bio::SearchIO.

DESCRIPTION

       This object is a subclass of Bio::SearchIO and provides some operations that facilitate working with CrossMatch and CrossMatch results.

       For general information about working with Results, see Bio::Search::Result::GenericResult.

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

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
       it. Please include a thorough description of the problem with code and data examples if at all possible.

   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 - Shin Leong
       Email sleong@watson.wustl.edu

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 a _

   next_result
	Title	: next_result
	Usage	: $result = stream->next_result
	Function: Reads the next ResultI object from the stream and returns it.

		  Certain driver modules may encounter entries in the stream that
		  are either misformatted or that use syntax not yet understood
		  by the driver. If such an incident is recoverable, e.g., by
		  dismissing a feature of a feature table or some other non-mandatory
		  part of an entry, the driver will issue a warning. In the case
		  of a non-recoverable situation an exception will be thrown.
		  Do not assume that you can resume parsing the same stream after
		  catching the exception. Note that you can always turn recoverable
		  errors into exceptions by calling $stream->verbose(2) (see
		  Bio::Root::RootI POD page).
	Returns : A Bio::Search::Result::ResultI object
	Args	: n/a

       See Bio::Root::RootI

   _alignment
	Title	: _alignment
	Usage	: private

   _parse
	Title	: _parse
	Usage	: private

   result_count
	Title	: result_count
	Usage	: $num = $stream->result_count;
	Function: Gets the number of CrossMatch results that have been parsed.
	Returns : integer
	Args	: none
	Throws	: none

perl v5.14.2							    2012-03-02					   Bio::SearchIO::cross_match(3pm)
Man Page