Provided by: libbio-perl-perl_1.7.8-1_all 
NAME
Bio::SearchIO::infernal - SearchIO-based Infernal parser
SYNOPSIS
my $parser = Bio::SearchIO->new(-format => 'infernal',
-file => 'purine.inf');
while( my $result = $parser->next_result ) {
# general result info, such as model used, Infernal version
while( my $hit = $result->next_hit ) {
while( my $hsp = $hit->next_hsp ) {
# ...
}
}
}
DESCRIPTION
This is a SearchIO-based parser for Infernal output from the cmsearch program. It
currently parses cmsearch output for Infernal versions 0.7-1.1; older versions may work
but will not be supported.
The latest version of Infernal is 1.1. The output has changed substantially relative to
version 1.0. Versions 1.x are stable releases (and output has stabilized) therefore it is
highly recommended that users upgrade to using the latest Infernal release. Support for
the older pre-v.1 developer releases will be dropped for future core 1.6 releases.
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 - Chris Fields
Email cjfields-at-uiuc-dot-edu
CONTRIBUTORS
Jeffrey Barrick, Michigan State University
Paul Cantalupo, University of Pittsburgh
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::infernal->new();
Function: Builds a new Bio::SearchIO::infernal object
Returns : Bio::SearchIO::infernal
Args : -fh/-file => cmsearch (infernal) filename
-format => 'infernal'
-model => query model (Rfam ID) (default undef)
-database => database name (default undef)
-query_acc => query accession, eg. Rfam accession RF####
-query_desc => query description, eg. Rfam description
-hsp_minscore => minimum HSP score cutoff
-convert_meta => boolean, set to convert meta string to simple WUSS format
-symbols => hash ref of structure symbols to use
(default symbols in %STRUCTURE_SYMBOLS hash)
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: Convenience method that calls start_element, characters, end_element
Returns : none
Args : Hash ref with the keys 'Name' and 'Data'
element_hash
Title : element
Usage : $eventhandler->element_hash({'Hsp_hit-from' => $start,
'Hsp_hit-to' => $end,
'Hsp_score' => $lastscore});
Function: Convenience method that takes multiple simple data elements and
maps to appropriate parameters
Returns : none
Args : Hash ref with the mapped key (in %MAPPING) and value
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 'within' because 'in' only
tests its immediate parent.
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
result_count
Title : result_count
Usage : my $count = $searchio->result_count
Function: Returns the number of results we have processed
Returns : integer
Args : none
model
Title : model
Usage : my $model = $parser->model();
Function: Get/Set model; Infernal currently does not output
the model name (Rfam ID)
Returns : String (name of model)
Args : [optional] String (name of model)
database
Title : database
Usage : my $database = $parser->database();
Function: Get/Set database; pre-v.1 versions of Infernal do not output
the database name
Returns : String (database name)
Args : [optional] String (database name)
algorithm
Title : algorithm
Usage : my $algorithm = $parser->algorithm();
Function: Get/Set algorithm; pre-v.1 versions of Infernal do not output
the algorithm name
Returns : String (algorithm name)
Args : [optional] String (algorithm name)
query_accession
Title : query_accession
Usage : my $acc = $parser->query_accession();
Function: Get/Set query (model) accession; pre-v1.1 Infernal does not output
the accession number (Rfam accession #)
Returns : String (accession)
Args : [optional] String (accession)
query_description
Title : query_description
Usage : my $acc = $parser->query_description();
Function: Get/Set query (model) description; pre-v1.1 Infernal does not output
the Rfam description
Returns : String (description)
Args : [optional] String (description)
hsp_minscore
Title : hsp_minscore
Usage : my $cutoff = $parser->hsp_minscore();
Function: Get/Set min bit score cutoff (for generating Hits/HSPs)
Returns : score (number)
Args : [optional] score (number)
convert_meta
Title : convert_meta
Usage : $parser->convert_meta(1);
Function: Get/Set boolean flag for converting Infernal WUSS format
to a simple bracketed format (simple WUSS by default)
Returns : boolean flag (TRUE or FALSE)
Args : [optional] boolean (eval's to TRUE or FALSE)
version
Title : version
Usage : $parser->version();
Function: Set the Infernal cmsearch version
Returns : version
Args : [optional] version
structure_symbols
Title : structure_symbols
Usage : my $hashref = $parser->structure_symbols();
Function: Get/Set RNA structure symbols
Returns : Hash ref of delimiters (5' stem, 3' stem, single-strand, etc)
: default = < (5-prime)
> (3-prime)
: (single-strand)
? (unknown)
. (gap)
Args : Hash ref of substitute delimiters, using above keys.
simple_meta
Title : simple_meta
Usage : my $string = $parser->simple_meta($str);
Function: converts more complex WUSS meta format into simple bracket format
using symbols defined in structure_symbols()
Returns : converted string
Args : [required] string to convert
Note : This is a very simple conversion method to get simple bracketed
format from Infernal data. If the convert_meta() flag is set,
this is the method used to convert the strings.