Bio::SearchIO::sim4.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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:
   http://bugzilla.open-bio.org/
 
 

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().