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 0.7-1.0; 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.
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 - Chris Fields¶
Email cjfields-at-uiuc-dot-edu
CONTRIBUTORS¶
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)
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.
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.