| Bio::SearchIO::exonerate(3pm) | User Contributed Perl Documentation | Bio::SearchIO::exonerate(3pm) |
Bio::SearchIO::exonerate - parser for Exonerate
# 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";
}
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)
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
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.
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
Email jason-at-bioperl.org
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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 obsolete 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.
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
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'
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'
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'
Title : characters Usage : $eventgenerator->characters($str) Function: Send a character events Returns : none Args : string
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
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
Title : start_document Usage : $eventgenerator->start_document Function: Handle a start document event Returns : none Args : none
Title : end_document Usage : $eventgenerator->end_document Function: Handles an end document event Returns : Bio::Search::Result::ResultI object Args : none
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)
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)
| 2021-08-15 | perl v5.32.1 |