Linux and UNIX Man Pages

Linux & Unix Commands - Search Man Pages

bio::search::result::hmmer3result(3pm) [debian man page]

Bio::Search::Result::hmmer3Result(3pm)			User Contributed Perl Documentation		    Bio::Search::Result::hmmer3Result(3pm)

NAME
Bio::Search::Result::hmmer3Result - DESCRIPTION of Object SYNOPSIS
Give standard usage here DESCRIPTION
Describe the object here 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 - Thomas Sharpton Email thomas.sharpton@gmail.com Describe contact details here CONTRIBUTORS
Additional contributors names and emails here 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 = new Bio::Search::Result::hmmer3Result.pm(); Function: Builds a new Bio::Search::Result::hmmer3Result.pm object Returns : an instance of Bio::Search::Result::hmmer3Result.pm Args : -hmm_name => string, name of hmm file -sequence_file => name of the sequence file hmm_name Title : hmm_name Usage : $obj->hmm_name($newval) Function: Get/Set the value of hmm_name Returns : value of hmm_name Args : newvalue (optional) sequence_file Title : sequence_file Usage : $obj->sequence_file($newval) Function: Get/Set the value of sequence_file Returns : value of sequence_file Args : newvalue (optional) next_model Title : next_model Usage : my $domain = $result->next_model Function: Returns the next domain - this is an alias for next_hit Returns : L<Bio::Search::Hit::HitI> object Args : none models Title : models Usage : my @domains = $result->models; Function: Returns the list of HMM models seen - this is an alias for hits() Returns : Array of L<Bio::Search::Hit::HitI> objects Args : none rewind Title : rewind Usage : $result->rewind; Function: Allow one to reset the Hit iteration to the beginning Since this is an in-memory implementation Returns : none Args : none perl v5.14.2 2012-03-02 Bio::Search::Result::hmmer3Result(3pm)

Check Out this Related Man Page

Bio::Search::Result::HmmpfamResult(3pm) 		User Contributed Perl Documentation		   Bio::Search::Result::HmmpfamResult(3pm)

NAME
Bio::Search::Result::HmmpfamResult - A parser and result object for hmmpfam results SYNOPSIS
# generally we use Bio::SearchIO to build these objects use Bio::SearchIO; my $in = Bio::SearchIO->new(-format => 'hmmer_pull', -file => 'result.hmmer'); while (my $result = $in->next_result) { print $result->query_name, " ", $result->algorithm, " ", $result->num_hits(), " hits "; } DESCRIPTION
This object implements a parser for hmmpfam result output, a program in the HMMER package. 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 - Sendu Bala Email bix@sendu.me.uk 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::Result::hmmpfam->new(); Function: Builds a new Bio::SearchIO::Result::hmmpfam object Returns : Bio::SearchIO::Result::hmmpfam Args : -chunk => [Bio::Root::IO, $start, $end] (required if no -parent) -parent => Bio::PullParserI object (required if no -chunk) -parameters => hash ref of search parameters (key => value), optional -statistics => hash ref of search statistics (key => value), optional where the array ref provided to -chunk contains an IO object for a filehandle to something representing the raw data of the result, and $start and $end define the tell() position within the filehandle that the result data starts and ends (optional; defaults to start and end of the entire thing described by the filehandle) next_hit Title : next_hit Usage : while( $hit = $result->next_hit()) { ... } Function: Returns the next available Hit object, representing potential matches between the query and various entities from the database. Returns : a Bio::Search::Hit::HitI object or undef if there are no more. Args : none next_model Title : next_model Usage : my $domain = $result->next_model Function: Returns the next domain - this is an alias for next_hit() Returns : L<Bio::Search::Hit::HitI> object Args : none hits Title : hits Usage : my @hits = $result->hits Function: Returns the HitI objects contained within this Result Returns : Array of Bio::Search::Hit::HitI objects Args : none See Also: Bio::Search::Hit::HitI models Title : models Usage : my @domains = $result->models; Function: Returns the list of HMM models seen - this is an alias for hits() Returns : Array of L<Bio::Search::Hit::HitI> objects Args : none sort_hits Title : sort_hits Usage : $result->sort_hits('<score') Function : Sorts the hits so that they come out in the desired order when hits() or next_hit() is called. Returns : n/a Args : A coderef for the sort function. See the documentation on the Perl sort() function for guidelines on writing sort functions. You will be sorting array references, not HitI objects. The references contain name as element 0, description as element 1, score as element 2, significance as element 3 and number of hsps as element 4. By default the sort order is ascending significance value (ie. most significant hits first). Note : To access the special variables $a and $b used by the Perl sort() function the user function must access Bio::Search::Result::HmmpfamResult namespace. For example, use : $result->sort_hits( sub{$Bio::Search::Result::HmmpfamResult::a->[2] <=> $Bio::Search::Result::HmmpfamResult::b->[2]}); NOT $result->sort_hits($a->[2] <=> $b->[2]); rewind Title : rewind Usage : $result->rewind; Function: Allow one to reset the Hit iterator to the beginning, so that next_hit() will subsequently return the first hit and so on. Returns : n/a Args : none perl v5.14.2 2012-03-02 Bio::Search::Result::HmmpfamResult(3pm)
Man Page