diff variant_effect_predictor/Bio/Search/Result/HMMERResult.pm @ 0:21066c0abaf5 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Search/Result/HMMERResult.pm	Fri Aug 03 10:04:48 2012 -0400
@@ -0,0 +1,445 @@
+# $Id: HMMERResult.pm,v 1.3 2002/10/22 07:45:18 lapp Exp $
+#
+# BioPerl module for Bio::Search::Result::HMMERResult
+#
+# Cared for by Jason Stajich <[e-mail]>
+#
+# Copyright Jason Stajich
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::Search::Result::HMMERResult - A Result object for HMMER results
+
+=head1 SYNOPSIS
+
+    use Bio::Search::Result::HMMERResult;
+    my $result = new Bio::Search::Result::HMMERResult
+    ( -hmm_name => 'pfam',
+      -sequence_file => 'roa1.pep',
+      -hits => \@hits);
+
+    # generally we use Bio::SearchIO to build these objects
+    use Bio::SearchIO;
+    my $in = new Bio::SearchIO(-format => 'hmmer',
+			       -file   => 'result.hmmer');
+    while( my $result = $in->next_result ) {
+	print $result->query_name, " ", $result->algorithm, " ", $result->num_hits(), " hits\n";
+    }
+
+=head1 DESCRIPTION
+
+This is a specialization of L<Bio::Search::Result::GenericResult>.
+There are a few extra methods, specifically L<sequence_file>,
+L<hmm_name>, L<next_models>, and L<models>.
+
+=head1 FEEDBACK
+
+=head2 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.
+
+  [e-mail]              - General discussion
+  http://bioperl.org/MailList.shtml  - About the mailing lists
+
+=head2 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
+email or the web:
+
+  [e-mail]
+  http://bugzilla.bioperl.org/
+
+=head1 AUTHOR - Jason Stajich
+
+Email [e-mail]
+
+Describe contact details here
+
+=head1 CONTRIBUTORS
+
+Additional contributors names and emails here
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object methods.
+Internal methods are usually preceded with a _
+
+=cut
+
+
+# Let the code begin...
+
+
+package Bio::Search::Result::HMMERResult;
+use vars qw(@ISA);
+use strict;
+
+use Bio::Search::Result::GenericResult;
+
+
+@ISA = qw(Bio::Search::Result::GenericResult );
+
+=head2 new
+
+ Title   : new
+ Usage   : my $obj = new Bio::Search::Result::HMMERResult();
+ Function: Builds a new Bio::Search::Result::HMMERResult object 
+ Returns : Bio::Search::Result::HMMERResult
+ Args    : -hmm_name => string, name of hmm file
+           -sequence_file => name of the sequence file
+
+plus Bio::Search::Result::GenericResult parameters
+
+           -query_name        => Name of query Sequence
+           -query_accession   => Query accession number (if available)
+           -query_description => Description of query sequence
+           -query_length      => Length of query sequence
+           -database_name     => Name of database
+           -database_letters  => Number of residues in database
+           -database_entries  => Number of entries in database
+           -parameters        => hash ref of search parameters (key => value)
+           -statistics        => hash ref of search statistics (key => value)
+           -algorithm         => program name (blastx)
+           -algorithm_version => version of the algorithm (2.1.2)
+           -program_reference => literature reference string for this algorithm
+
+=cut
+
+sub new {
+  my($class,@args) = @_;
+  my $self = $class->SUPER::new(@args);
+  
+  my ($hmm,$seqfile) = $self->_rearrange([qw(HMM_NAME SEQUENCE_FILE)],
+					 @args);
+  
+  defined( $seqfile) && $self->sequence_file($seqfile);
+  defined( $hmm) && $self->hmm_name($hmm);
+
+  return $self;
+}
+
+
+=head2 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)
+
+
+=cut
+
+sub hmm_name{
+   my ($self,$value) = @_;
+   if( defined $value) {
+      $self->{'_hmm_name'} = $value;
+    }
+    return $self->{'_hmm_name'};
+}
+
+
+=head2 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)
+
+
+=cut
+
+sub sequence_file{
+   my ($self,$value) = @_;
+   if( defined $value) {
+      $self->{'_sequence_file'} = $value;
+    }
+    return $self->{'_sequence_file'};
+
+}
+
+
+=head2 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
+
+
+=cut
+
+sub next_model{ shift->next_hit }
+
+=head2 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
+
+
+=cut
+
+sub models{ shift->hits }
+
+=head2 Bio::Search::Result::GenericResult inherited methods
+
+=cut
+
+=head2 algorithm
+
+ Title   : algorithm
+ Usage   : my $r_type = $hsp->algorithm
+ Function: Obtain the name of the algorithm used to obtain the Result
+ Returns : string (e.g., BLASTP)
+ Args    : [optional] scalar string to set value
+
+=cut
+
+=head2 algorithm_version
+
+ Title   : algorithm_version
+ Usage   : my $r_version = $hsp->algorithm_version
+ Function: Obtain the version of the algorithm used to obtain the Result
+ Returns : string (e.g., 2.1.2)
+ Args    : [optional] scalar string to set algorithm version value
+
+=cut
+
+=head2 Bio::Search::Result::ResultI interface methods
+
+Bio::Search::Result::ResultI implementation
+
+=head2 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
+
+
+=cut
+
+=head2 query_name
+
+ Title   : query_name
+ Usage   : $id = $result->query_name();
+ Function: Get the string identifier of the query used by the
+           algorithm that performed the search.
+ Returns : a string.
+ Args    : [optional] new string value for query name
+
+=cut
+
+=head2 query_accession
+
+ Title   : query_accession
+ Usage   : $id = $result->query_accession();
+ Function: Get the accession (if available) for the query sequence
+ Returns : a string
+ Args    : [optional] new string value for accession
+
+=cut
+
+=head2 query_length
+
+ Title   : query_length
+ Usage   : $id = $result->query_length();
+ Function: Get the length of the query sequence
+           used in the search.
+ Returns : a number
+ Args    :  [optional] new integer value for query length
+
+=cut
+
+=head2 query_description
+
+ Title   : query_description
+ Usage   : $id = $result->query_description();
+ Function: Get the description of the query sequence
+           used in the search.
+ Returns : a string
+ Args    : [optional] new string for the query description
+
+=cut
+
+=head2 database_name
+
+ Title   : database_name
+ Usage   : $name = $result->database_name()
+ Function: Used to obtain the name of the database that the query was searched
+           against by the algorithm.
+ Returns : a scalar string
+ Args    : [optional] new string for the db name
+
+=cut
+
+=head2 database_letters
+
+ Title   : database_letters
+ Usage   : $size = $result->database_letters()
+ Function: Used to obtain the size of database that was searched against.
+ Returns : a scalar integer (units specific to algorithm, but probably the
+           total number of residues in the database, if available) or undef if
+           the information was not available to the Processor object.
+ Args    : [optional] new scalar integer for number of letters in db 
+
+
+=cut
+
+=head2 database_entries
+
+ Title   : database_entries
+ Usage   : $num_entries = $result->database_entries()
+ Function: Used to obtain the number of entries contained in the database.
+ Returns : a scalar integer representing the number of entities in the database
+           or undef if the information was not available.
+ Args    : [optional] new integer for the number of sequence entries in the db
+
+
+=cut
+
+=head2 get_parameter
+
+ Title   : get_parameter
+ Usage   : my $gap_ext = $report->get_parameter('gapext')
+ Function: Returns the value for a specific parameter used
+           when running this report
+ Returns : string
+ Args    : name of parameter (string)
+
+=cut
+
+=head2 available_parameters
+
+ Title   : available_parameters
+ Usage   : my @params = $report->available_paramters
+ Function: Returns the names of the available parameters
+ Returns : Return list of available parameters used for this report
+ Args    : none
+
+=cut
+
+=head2 get_statistic
+
+ Title   : get_statistic
+ Usage   : my $gap_ext = $report->get_statistic('kappa')
+ Function: Returns the value for a specific statistic available 
+           from this report
+ Returns : string
+ Args    : name of statistic (string)
+
+=cut
+
+=head2 available_statistics
+
+ Title   : available_statistics
+ Usage   : my @statnames = $report->available_statistics
+ Function: Returns the names of the available statistics
+ Returns : Return list of available statistics used for this report
+ Args    : none
+
+=cut
+
+=head2 Bio::Search::Result::GenericResult specific methods
+
+=cut
+
+=head2 add_hit
+
+ Title   : add_hit
+ Usage   : $report->add_hit($hit)
+ Function: Adds a HitI to the stored list of hits
+ Returns : Number of HitI currently stored
+ Args    : Bio::Search::Hit::HitI
+
+=cut
+
+=head2 rewind
+
+ Title   : rewind
+ Usage   : $result->rewind;
+ Function: Allow one to reset the Hit iteration to the beginning
+           Since this is an in-memory implementation
+ Returns : none
+ Args    : none
+
+=cut
+
+sub rewind{
+   my ($self) = @_;
+   $self->{'_hitindex'} = 0;
+}
+
+
+=head2 add_parameter
+
+ Title   : add_parameter
+ Usage   : $report->add_parameter('gapext', 11);
+ Function: Adds a parameter
+ Returns : none
+ Args    : key  - key value name for this parama
+           value - value for this parameter
+
+=cut
+
+=head2 add_statistic
+
+ Title   : add_statistic
+ Usage   : $report->add_statistic('lambda', 2.3);
+ Function: Adds a parameter
+ Returns : none
+ Args    : key  - key value name for this parama
+           value - value for this parameter
+
+=cut
+
+=head2 num_hits
+
+ Title   : num_hits
+ Usage   : my $hitcount= $result->num_hits
+ Function: returns the number of hits for this query result
+ Returns : integer
+ Args    : none
+
+
+=cut
+
+=head2 hits
+
+ Title   : hits
+ Usage   : my @hits = $result->hits
+ Function: Returns the available hits for this Result
+ Returns : Array of L<Bio::Search::Hit::HitI> objects
+ Args    : none
+
+
+=cut
+
+=head2 program_reference
+
+ Title   : program_reference
+ Usage   : $obj->program_reference($newval)
+ Function: 
+ Returns : value of the literature reference for the algorithm
+ Args    : newvalue (optional)
+
+
+=cut
+
+1;