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.

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://github.com/bioperl/bioperl-live/issues

AUTHOR - Jason Stajich, Aaron Mackey, William Pearson

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 (6), 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().

_processHits

Title   : _processHits
Usage   : Private method. For internal use only.
Function: Process/report any hits/hsps we saw in the top table, not in alignments.
Returns : nothing.
Args    : array of hits to process.

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq