Bio::SearchIO::sim4(3pm) User Contributed Perl Documentation Bio::SearchIO::sim4(3pm)
NAME
Bio::SearchIO::sim4 - parser for Sim4 alignments
SYNOPSIS
# do not use this module directly, it is a driver for SearchIO
use Bio::SearchIO;
my $searchio = Bio::SearchIO->new(-file => 'results.sim4',
-format => 'sim4');
while ( my $result = $searchio->next_result ) {
while ( my $hit = $result->next_hit ) {
while ( my $hsp = $hit->next_hsp ) {
# ...
}
}
}
DESCRIPTION
This is a driver for the SearchIO system for parsing Sim4. http://globin.cse.psu.edu/html/docs/sim4.html
Cannot parse LAV or 'exon file' formats (A=2 or A=5)
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-dot-org
CONTRIBUTORS
Luc Gauthier (lgauthie@hotmail.com)
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::sim4->new();
Function: Builds a new Bio::SearchIO::sim4 object
Returns : an instance of Bio::SearchIO::sim4
Args :
next_result
Title : next_result
Usage : my $result = $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
_will_handle
Title : _will_handle
Usage : Private method. For internal use only.
if( $self->_will_handle($type) ) { ... }
Function: Provides an optimized way to check whether or not an element of a
given type is to be handled.
Returns : Reference to EventHandler object if the element type is to be handled.
undef if the element type is not to be handled.
Args : string containing type of element.
Optimizations:
1. Using the cached pointer to the EventHandler to minimize repeated lookups.
2. Caching the will_handle status for each type that is encountered
so that it only need be checked by calling handler->will_handle($type) once.
This does not lead to a major savings by itself (only 5-10%). In combination with other optimizations, or for large parse jobs, the
savings good be significant.
To test against the unoptimized version, remove the parentheses from around the third term in the ternary " ? : " operator and add two
calls to $self->_eventHandler().
perl v5.14.2 2012-03-02 Bio::SearchIO::sim4(3pm)