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