Bio::SearchIO::fasta(3pm) User Contributed Perl Documentation Bio::SearchIO::fasta(3pm)
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:
https://redmine.open-bio.org/projects/bioperl/
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.
perl v5.14.2 2012-03-02 Bio::SearchIO::fasta(3pm)