diff variant_effect_predictor/Bio/Search/HSP/HMMERHSP.pm @ 0:1f6dce3d34e0

Uploaded

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+++ b/variant_effect_predictor/Bio/Search/HSP/HMMERHSP.pm	Thu Apr 11 02:01:53 2013 -0400
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+# $Id: HMMERHSP.pm,v 1.3 2002/10/22 07:45:17 lapp Exp $
+#
+# BioPerl module for Bio::Search::HSP::HMMERHSP
+#
+# 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::HSP::HMMERHSP - A HSP object for HMMER results
+
+=head1 SYNOPSIS
+
+    use Bio::Search::HSP::HMMERHSP;
+    # us it just like a Bio::Search::HSP::GenericHSP object
+
+=head1 DESCRIPTION
+
+This object is a specialization of L<Bio::Search::HSP::GenericHSP>.
+
+=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::HSP::HMMERHSP;
+use vars qw(@ISA);
+use strict;
+use Bio::Search::HSP::GenericHSP;
+
+@ISA = qw(Bio::Search::HSP::GenericHSP);
+
+=head2 new
+
+ Title   : new
+ Usage   : my $obj = new Bio::Search::HSP::HMMERHSP();
+ Function: Builds a new Bio::Search::HSP::HMMERHSP object 
+ Returns : Bio::Search::HSP::HMMERHSP
+ Args    :
+
+Plus Bio::Seach::HSP::GenericHSP methods
+
+           -algorithm => algorithm used (BLASTP, TBLASTX, FASTX, etc)
+           -evalue    => evalue
+           -pvalue    => pvalue
+           -bits      => bit value for HSP
+           -score     => score value for HSP (typically z-score but depends on
+					      analysis)
+           -hsp_length=> Length of the HSP (including gaps)
+           -identical => # of residues that that matched identically
+           -conserved => # of residues that matched conservatively 
+                           (only protein comparisions; 
+			    conserved == identical in nucleotide comparisons)
+           -hsp_gaps   => # of gaps in the HSP
+           -query_gaps => # of gaps in the query in the alignment
+           -hit_gaps   => # of gaps in the subject in the alignment    
+           -query_name  => HSP Query sequence name (if available)
+           -query_start => HSP Query start (in original query sequence coords)
+           -query_end   => HSP Query end (in original query sequence coords)
+           -hit_name    => HSP Hit sequence name (if available)
+           -hit_start   => HSP Hit start (in original hit sequence coords)
+           -hit_end     => HSP Hit end (in original hit sequence coords)
+           -hit_length  => total length of the hit sequence
+           -query_length=> total length of the query sequence
+           -query_seq   => query sequence portion of the HSP
+           -hit_seq     => hit sequence portion of the HSP
+           -homology_seq=> homology sequence for the HSP
+           -hit_frame   => hit frame (only if hit is translated protein)
+           -query_frame => query frame (only if query is translated protein)
+
+=cut
+
+=head2 Bio::Search::HSP::HSPI methods
+
+Implementation of Bio::Search::HSP::HSPI methods follow
+
+=head2 algorithm
+
+ Title   : algorithm
+ Usage   : my $r_type = $hsp->algorithm
+ Function: Obtain the name of the algorithm used to obtain the HSP
+ Returns : string (e.g., BLASTP)
+ Args    : [optional] scalar string to set value
+
+=cut
+
+=head2 pvalue
+
+ Title   : pvalue
+ Usage   : my $pvalue = $hsp->pvalue();
+ Function: Returns the P-value for this HSP or undef 
+ Returns : float or exponential (2e-10)
+           P-value is not defined with NCBI Blast2 reports.
+ Args    : [optional] numeric to set value
+
+=cut
+
+=head2 evalue
+
+ Title   : evalue
+ Usage   : my $evalue = $hsp->evalue();
+ Function: Returns the e-value for this HSP
+ Returns : float or exponential (2e-10)
+ Args    : [optional] numeric to set value
+
+=cut
+
+=head2 frac_identical
+
+ Title   : frac_identical
+ Usage   : my $frac_id = $hsp->frac_identical( ['query'|'hit'|'total'] );
+ Function: Returns the fraction of identitical positions for this HSP 
+ Returns : Float in range 0.0 -> 1.0
+ Args    : arg 1:  'query' = num identical / length of query seq (without gaps)
+                   'hit'   = num identical / length of hit seq (without gaps)
+                   'total' = num identical / length of alignment (with gaps)
+                   default = 'total' 
+           arg 2: [optional] frac identical value to set for the type requested
+
+=cut
+
+=head2 frac_conserved
+
+ Title    : frac_conserved
+ Usage    : my $frac_cons = $hsp->frac_conserved( ['query'|'hit'|'total'] );
+ Function : Returns the fraction of conserved positions for this HSP.
+            This is the fraction of symbols in the alignment with a 
+            positive score.
+ Returns : Float in range 0.0 -> 1.0
+ Args    : arg 1: 'query' = num conserved / length of query seq (without gaps)
+                  'hit'   = num conserved / length of hit seq (without gaps)
+                  'total' = num conserved / length of alignment (with gaps)
+                  default = 'total' 
+           arg 2: [optional] frac conserved value to set for the type requested
+
+=cut
+
+=head2 gaps
+
+ Title    : gaps
+ Usage    : my $gaps = $hsp->gaps( ['query'|'hit'|'total'] );
+ Function : Get the number of gaps in the query, hit, or total alignment.
+ Returns  : Integer, number of gaps or 0 if none
+ Args     : arg 1: 'query' = num gaps in query seq
+                   'hit'   = num gaps in hit seq
+                   'total' = num gaps in whole alignment 
+                   default = 'total' 
+            arg 2: [optional] integer gap value to set for the type requested
+
+=cut
+
+=head2 query_string
+
+ Title   : query_string
+ Usage   : my $qseq = $hsp->query_string;
+ Function: Retrieves the query sequence of this HSP as a string
+ Returns : string
+ Args    : [optional] string to set for query sequence
+
+
+=cut
+
+=head2 hit_string
+
+ Title   : hit_string
+ Usage   : my $hseq = $hsp->hit_string;
+ Function: Retrieves the hit sequence of this HSP as a string
+ Returns : string
+ Args    : [optional] string to set for hit sequence
+
+
+=cut
+
+
+=head2 homology_string
+
+ Title   : homology_string
+ Usage   : my $homo_string = $hsp->homology_string;
+ Function: Retrieves the homology sequence for this HSP as a string.
+         : The homology sequence is the string of symbols in between the 
+         : query and hit sequences in the alignment indicating the degree
+         : of conservation (e.g., identical, similar, not similar).
+ Returns : string
+ Args    : [optional] string to set for homology sequence
+
+=cut
+
+=head2 length
+
+ Title    : length
+ Usage    : my $len = $hsp->length( ['query'|'hit'|'total'] );
+ Function : Returns the length of the query or hit in the alignment 
+            (without gaps) 
+            or the aggregate length of the HSP (including gaps;
+            this may be greater than either hit or query )
+ Returns  : integer
+ Args     : arg 1: 'query' = length of query seq (without gaps)
+                   'hit'   = length of hit seq (without gaps)
+                   'total' = length of alignment (with gaps)
+                   default = 'total' 
+            arg 2: [optional] integer length value to set for specific type
+
+=cut
+
+=head2 percent_identity
+
+ Title   : percent_identity
+ Usage   : my $percentid = $hsp->percent_identity()
+ Function: Returns the calculated percent identity for an HSP
+ Returns : floating point between 0 and 100 
+ Args    : none
+
+
+=cut
+
+
+=head2 frame
+
+ Title   : frame
+ Usage   : $hsp->frame($queryframe,$subjectframe)
+ Function: Set the Frame for both query and subject and insure that
+           they agree.
+           This overrides the frame() method implementation in
+           FeaturePair.
+ Returns : array of query and subjects if return type wants an array
+           or query frame if defined or subject frame
+ Args    : none
+ Note    : Frames are stored in the GFF way (0-2) not 1-3
+           as they are in BLAST (negative frames are deduced by checking 
+				 the strand of the query or hit)
+
+=cut
+
+
+=head2 get_aln
+
+ Title   : get_aln
+ Usage   : my $aln = $hsp->gel_aln
+ Function: Returns a Bio::SimpleAlign representing the HSP alignment
+ Returns : Bio::SimpleAlign
+ Args    : none
+
+=cut
+
+sub get_aln {
+    my ($self) = shift;
+    $self->warn("Innapropriate to build a Bio::SimpleAlign from a HMMER HSP object");
+    return undef;
+}
+
+=head2 num_conserved
+
+ Title   : num_conserved
+ Usage   : $obj->num_conserved($newval)
+ Function: returns the number of conserved residues in the alignment
+ Returns : inetger
+ Args    : integer (optional)
+
+
+=cut
+
+=head2 num_identical
+
+ Title   : num_identical
+ Usage   : $obj->num_identical($newval)
+ Function: returns the number of identical residues in the alignment
+ Returns : integer
+ Args    : integer (optional)
+
+
+=cut
+
+=head2 seq_inds
+
+ Title   : seq_inds
+ Purpose   : Get a list of residue positions (indices) for all identical 
+           : or conserved residues in the query or sbjct sequence.
+ Example   : @s_ind = $hsp->seq_inds('query', 'identical');
+           : @h_ind = $hsp->seq_inds('hit', 'conserved');
+           : @h_ind = $hsp->seq_inds('hit', 'conserved', 1);
+ Returns   : List of integers 
+           : May include ranges if collapse is true.
+ Argument  : seq_type  = 'query' or 'hit' or 'sbjct'  (default = query)
+           :  ('sbjct' is synonymous with 'hit') 
+           : class     = 'identical' or 'conserved' or 'nomatch' or 'gap'
+           :              (default = identical)
+           :              (can be shortened to 'id' or 'cons')
+           :              
+           : collapse  = boolean, if true, consecutive positions are merged
+           :             using a range notation, e.g., "1 2 3 4 5 7 9 10 11" 
+           :             collapses to "1-5 7 9-11". This is useful for 
+           :             consolidating long lists. Default = no collapse.
+ Throws    : n/a.
+ Comments  : 
+
+See Also   : L<Bio::Search::BlastUtils::collapse_nums()|Bio::Search::BlastUtils>, L<Bio::Search::Hit::HitI::seq_inds()|Bio::Search::Hit::HitI>
+
+=cut
+
+=head2 Inherited from Bio::SeqFeature::SimilarityPair
+
+These methods come from Bio::SeqFeature::SimilarityPair
+
+=head2 query
+
+ Title   : query
+ Usage   : my $query = $hsp->query
+ Function: Returns a SeqFeature representing the query in the HSP
+ Returns : Bio::SeqFeature::Similarity
+ Args    : [optional] new value to set
+
+
+=head2 hit
+
+ Title   : hit
+ Usage   : my $hit = $hsp->hit
+ Function: Returns a SeqFeature representing the hit in the HSP
+ Returns : Bio::SeqFeature::Similarity
+ Args    : [optional] new value to set
+
+
+=head2 significance
+
+ Title   : significance
+ Usage   : $evalue = $obj->significance();
+           $obj->significance($evalue);
+ Function: Get/Set the significance value
+ Returns : numeric
+ Args    : [optional] new value to set
+
+
+=head2 score
+
+ Title   : score
+ Usage   : my $score = $hsp->score();
+ Function: Returns the score for this HSP or undef 
+ Returns : numeric           
+ Args    : [optional] numeric to set value
+
+=cut 
+
+=head2 bits
+
+ Title   : bits
+ Usage   : my $bits = $hsp->bits();
+ Function: Returns the bit value for this HSP or undef 
+ Returns : numeric
+ Args    : none
+
+=cut
+
+
+1;