Provided by: libbio-perl-perl_1.6.923-1_all bug

NAME

       Bio::SearchIO::exonerate - parser for Exonerate

SYNOPSIS

         # do not use this module directly, it is a driver for SearchIO

         use Bio::SearchIO;
         my $searchio = Bio::SearchIO->new(-file => 'file.exonerate',
                                          -format => 'exonerate');

         while( my $r = $searchio->next_result ) {
           print $r->query_name, "\n";
         }

DESCRIPTION

       This is a driver for the SearchIO system for parsing Exonerate (Guy Slater) output.  You
       can get Exonerate at http://www.ebi.ac.uk/~guy/exonerate/ [until Guy puts up a Web
       reference,publication for it.]).

       An optional parameter -min_intron is supported by the new initialization method.  This is
       if you run Exonerate with a different minimum intron length (default is 30) the parser
       will be able to detect the difference between standard deletions and an intron.  Still
       some room to play with there that might cause this to get misinterpreted that has not been
       fully tested or explored.

       The VULGAR and CIGAR formats should be parsed okay now creating HSPs where appropriate (so
       merging match states where appropriate rather than breaking an HSP at each indel as it may
       have done in the past).  The GFF that comes from exonerate is still probably a better way
       to go if you are doing protein2genome or est2genome mapping.  For example you can see this
       script:

       ### TODO: Jason, this link is dead, do we have an updated one?
       http://fungal.genome.duke.edu/~jes12/software/scripts/process_exonerate_gff3.perl.txt

       If your report contains both CIGAR and VULGAR lines only the first one will processed for
       a given Query/Target pair.  If you preferentially want to use VULGAR or CIGAR add one of
       these options when initializing the SearchIO object.

           -cigar  => 1
       OR
           -vulgar => 1

       Or set them via these methods.

           $parser->cigar(1)
       OR
           $parser->vulgar(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

   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 - Jason Stajich

       Email jason-at-bioperl.org

APPENDIX

       The rest of the documentation details each of the object methods.  Internal methods are
       usually preceded with a _

   new
        Title   : new
        Usage   : my $obj = Bio::SearchIO::exonerate->new();
        Function: Builds a new Bio::SearchIO::exonerate object
        Returns : an instance of Bio::SearchIO::exonerate
        Args    : -min_intron => somewhat obselete option, how to determine if a
                                 an indel is an intron or a local gap.  Use VULGAR
                                 rather than CIGAR to avoid this heuristic,default 30.
                  -cigar       => 1   set this to 1 if you want to parse
                                      CIGAR exclusively.
                  -vulgar      => 1   set this to 1 if you want to parse VULGAR
                                      exclusively, setting both to 1 will revert
                                      to the default behavior of just parsing the
                                      first line that it sees.

   next_result
        Title   : next_result
        Usage   : my $hit = $searchio->next_result;
        Function: Returns the next Result from a search
        Returns : Bio::Search::Result::ResultI object
        Args    : none

   start_element
        Title   : start_element
        Usage   : $eventgenerator->start_element
        Function: Handles a start element event
        Returns : none
        Args    : hashref with at least 2 keys 'Data' and 'Name'

   end_element
        Title   : start_element
        Usage   : $eventgenerator->end_element
        Function: Handles an end element event
        Returns : none
        Args    : hashref with at least 2 keys 'Data' and 'Name'

   element
        Title   : element
        Usage   : $eventhandler->element({'Name' => $name, 'Data' => $str});
        Function: Convience method that calls start_element, characters, end_element
        Returns : none
        Args    : Hash ref with the keys 'Name' and 'Data'

   characters
        Title   : characters
        Usage   : $eventgenerator->characters($str)
        Function: Send a character events
        Returns : none
        Args    : string

   within_element
        Title   : within_element
        Usage   : if( $eventgenerator->within_element($element) ) {}
        Function: Test if we are within a particular element
                  This is different than 'in' because within can be tested
                  for a whole block.
        Returns : boolean
        Args    : string element name

   in_element
        Title   : in_element
        Usage   : if( $eventgenerator->in_element($element) ) {}
        Function: Test if we are in a particular element
                  This is different than 'in' because within can be tested
                  for a whole block.
        Returns : boolean
        Args    : string element name

   start_document
        Title   : start_document
        Usage   : $eventgenerator->start_document
        Function: Handle a start document event
        Returns : none
        Args    : none

   end_document
        Title   : end_document
        Usage   : $eventgenerator->end_document
        Function: Handles an end document event
        Returns : Bio::Search::Result::ResultI object
        Args    : none

   vulgar
        Title   : vulgar
        Usage   : $obj->vulgar($newval)
        Function: Get/Set flag, do you want to build HSPs from VULGAR string?
        Returns : value of vulgar (a scalar)
        Args    : on set, new value (a scalar or undef, optional)

   cigar
        Title   : cigar
        Usage   : $obj->cigar($newval)
        Function: Get/Set boolean flag do you want to build HSPs from CIGAR strings?
        Returns : value of cigar (a scalar)
        Args    : on set, new value (a scalar or undef, optional)