/ 
BioPerl-1.007000_004
River stage two • 60 direct dependents • 65 total dependents
/ Bio::SearchIO::exonerate

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

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)