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 0.7-1.0; older versions may work but will not be supported.As the first stable version has been released (and output has stabilized) 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.
[email protected] - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list: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-eduCONTRIBUTORS
Jeffrey Barrick, Michigan State University
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; Infernal currently does 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; current 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; Infernal currently 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; Infernal currently 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.