Bio::SearchIO::fasta.3pm

Langue: en

Version: 2010-04-29 (fedora - 01/12/10)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::SearchIO::fasta - A SearchIO parser for FASTA results

SYNOPSIS

   # Do not use this object directly, use it through the SearchIO system
    use Bio::SearchIO;
    my $searchio = Bio::SearchIO->new(-format => 'fasta',
                     -file   => 'report.FASTA');
    while( my $result = $searchio->next_result ) {
     # ... do what you would normally doi with Bio::SearchIO.
    }
 
 

DESCRIPTION

This object contains the event based parsing code for FASTA format reports. It creates Bio::Search::HSP::FastaHSP objects instead of Bio::Search::HSP::GenericHSP for the HSP objects.

This module will parse -m 9 -d 0 output as well as default m 1 output from FASTA as well as SSEARCH.

Also see the SearchIO HOWTO: http://bioperl.open-bio.org/wiki/HOWTO:SearchIO <http://bioperl.open-bio.org/wiki/HOWTO:SearchIO>.

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, Aaron Mackey

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::fasta->new();
  Function: Builds a new Bio::SearchIO::fasta object 
  Returns : Bio::SearchIO::fasta
  Args    : -idlength - set ID length to something other 
                        than the default (7), this is only
                        necessary if you have compiled FASTA
                        with a new default id length to display
                        in the HSP alignment blocks
 
 

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
 
 

_mode

  Title   : _mode
  Usage   : $obj->_mode($newval)
  Function: 
  Example : 
  Returns : value of _mode
  Args    : newvalue (optional)
 
 

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: Handles 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
 
 

idlength

  Title   : idlength
  Usage   : $obj->idlength($newval)
  Function: Internal storage of the length of the ID desc
            in the HSP alignment blocks.  Defaults to
            $IDLENGTH class variable value
  Returns : value of idlength
  Args    : newvalue (optional)
 
 

result_count

  Title   : result_count
  Usage   : my $count = $searchio->result_count
  Function: Returns the number of results we have processed
  Returns : integer
  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().