diff variant_effect_predictor/Bio/EnsEMBL/Utils/CigarString.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/Utils/CigarString.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,350 @@
+=head1 LICENSE
+
+  Copyright (c) 1999-2012 The European Bioinformatics Institute and
+  Genome Research Limited.  All rights reserved.
+
+  This software is distributed under a modified Apache license.
+  For license details, please see
+
+    http://www.ensembl.org/info/about/code_licence.html
+
+=head1 CONTACT
+
+  Please email comments or questions to the public Ensembl
+  developers list at <[e-mail]>.
+
+  Questions may also be sent to the Ensembl help desk at
+  <[e-mail]>.
+
+=head1 AUTHOR
+
+Juguang Xiao <[e-mail]>
+
+=cut
+
+=head1 NAME
+
+Bio::EnsEMBL::Utils::CigarString, a utilites module to generate cigar
+strings
+
+=head1 DESCRIPTION
+
+Sequence alignment hits were previously stored within the core database
+as ungapped alignments. This imposed 2 major constraints on alignments:
+
+a) alignments for a single hit record would require multiple rows in the
+   database, and
+b) it was not possible to accurately retrieve the exact original
+   alignment.
+
+Therefore, in the new branch sequence alignments are now stored as
+ungapped alignments in the cigar line format (where CIGAR stands for
+Concise Idiosyncratic Gapped Alignment Report).
+
+In the cigar line format alignments are sotred as follows:
+
+  M: Match
+  D: Deletino
+  I: Insertion
+
+An example of an alignment for a hypthetical protein match is shown
+below:
+
+
+  Query:   42 PGPAGLP----GSVGLQGPRGLRGPLP-GPLGPPL...
+              PG    P    G     GP   R      PLGP
+  Sbjct: 1672 PGTP*TPLVPLGPWVPLGPSSPR--LPSGPLGPTD...
+
+protein_align_feature table as the following cigar line:
+
+  7M4D12M2I2MD7M 
+
+=cut
+
+package Bio::EnsEMBL::Utils::CigarString;
+
+use strict;
+use vars qw(@ISA);
+use Bio::EnsEMBL::Root;
+
+@ISA = qw(Bio::EnsEMBL::Root);
+
+=head2 split_hsp
+
+    Name  : split_hsp (this name is derived from the original sub in BlastWorn)
+    Usage : my $hsp; # a ready Bio::Search::HSP::GenericHSP object.
+my $factory = new Bio::EnsEMBL::Utils::CigarString;
+my $cigar_string = $factory->split_hsp($hsp);
+  
+    Function: generate cigar string.
+    Argument: a HSP object.
+    Returns : a text string.
+  
+=cut
+
+sub split_hsp {
+    my ($self, $hsp) = @_;
+
+    $self->throw("a defined object needed") unless($hsp && defined($hsp));
+    unless(ref($hsp) && $hsp->isa('Bio::Search::HSP::GenericHSP')){
+        $self->throw("a HSP object needed");
+    }
+
+    my ($qtype, $htype) = $self->_findTypes($hsp);
+    my ($qstrand, $hstrand) = $self->_findStrands($hsp);
+    my ($qinc, $hinc) = $self->_findIncrements($qstrand,$hstrand,$qtype,$htype);
+
+    my @gaps = ();
+    my @qchars = split(//, $hsp->query_string);
+    my @hchars = split(//, $hsp->hit_string);
+    my $qstart;
+    if($qstrand == 1){
+        $qstart = $hsp->query->start;
+    }elsif($qstart == -1){
+        $qstart = $hsp->query->end;
+    }else{
+        $self->warn("[$qstart], invalid strand value on query");
+        $qstart = $hsp->query->start; 
+        # Is this a SearchIO's bug???
+    }
+    
+    my $hstart; 
+    if($hstrand == 1){
+        $hstart = $hsp->subject->start;
+    }elsif($hstrand != -1){
+        $hstart = $hsp->subject->end;
+    }else{
+        $self->throw("[$hstart], invalid strand value on subject");
+    }
+
+    my $qend = $qstart;
+    my $hend = $hstart;
+    my $count = 0;
+    my $found = 0;
+
+    my @align_coordinates = ();
+    while($count <= $#qchars){
+        if($qchars[$count] ne '-' && $hchars[$count] ne '-') {
+            $qend += $qinc;
+            $hend += $hinc;
+            $found = 1;
+        }else{ # gapped region
+            push(@align_coordinates, [$qstart, $hstart]) if($found == 1);
+
+            $qstart = $qend;
+            $qstart += $qinc if($qchars[$count] ne '-');
+
+            $hstart = $hend;
+            $hstart += $hinc if($hchars[$count] ne '-');
+
+            $qend = $qstart;
+            $hend = $hstart;
+            $found = 0;
+        }
+        $count++;
+    }
+
+    if($found){
+        push(@align_coordinates, [$qstart, $hstart]);
+    }
+
+    my $cigar_string = "";
+    my $last = $#align_coordinates;
+    if($last >= 0){
+        for(my $i=0; $i<$last; $i++){
+            my $q_this_start = $align_coordinates[$i]->[0];
+            my $q_next_start = $align_coordinates[$i+1]->[0];
+            my $q_length = ($q_next_start-$q_this_start-1)*$qinc;
+            $q_length = abs($q_length);
+            my $h_this_start = $align_coordinates[$i]->[1];
+            my $h_next_start = $align_coordinates[$i+1]->[1];
+            my $h_length = ($h_next_start-$h_this_start-1)*$hinc;
+            $h_length = abs($h_length);
+
+            my $diff = $q_length - $h_length;
+            if($diff > 0){ # Insertion
+                $cigar_string .= $diff unless($diff == 1);
+                $cigar_string .= 'I';
+            }elsif($diff < 0){ # Deletion
+                $cigar_string .= -$diff unless($diff == -1);
+                $cigar_string .= 'D';
+            }else{ # e.g $diff == 0, Match
+                $cigar_string .= $q_length unless($q_length == 1);
+                $cigar_string .= 'M';
+            }
+                
+        } # for
+    } # if
+    
+    return $cigar_string;
+}
+
+
+sub _findStrands {
+    my ($self,$hsp) = @_;
+    
+    my $qstrand = $hsp->query->strand;
+    unless($qstrand == 1 || $qstrand == -1){
+        $self->warn("query's strand value is neither 1 or -1");
+        $qstrand = 1;
+    }
+    
+    my $hstrand = $hsp->subject->strand;
+    unless($hstrand == 1 || $hstrand == -1){
+        $self->warn("subject's strand value is neither 1 or -1");
+        $hstrand = 1;
+    }
+    
+    return ( $qstrand, $hstrand);
+}
+
+sub _findTypes {
+    my ($self,$hsp) = @_;
+
+    my $type1;
+    my $type2;
+    my $len1 = $hsp->query->length();
+    my $len2 = $hsp->subject->length();
+
+    if ($len1/$len2 > 2) {
+        $type1 = 'dna';
+        $type2 = 'pep';
+    } elsif ($len2/$len1 > 2) {
+        $type1 = 'pep';
+        $type2 = 'dna';
+    } else {
+        $type1 = 'dna';
+        $type2 = 'dna';
+    }
+
+    return ($type1,$type2);
+}
+
+sub _findIncrements {
+    my ($self,$qstrand,$hstrand,$qtype,$htype) = @_;
+
+    my $qinc   = 1 * $qstrand;
+    my $hinc   = 1 * $hstrand;
+
+    if ($qtype eq 'dna' && $htype eq 'pep') {
+    $qinc = 3 * $qinc;
+    }
+    if ($qtype eq 'pep' && $htype eq 'dna') {
+    $hinc = 3 * $hinc;
+    }
+
+    return ($qinc,$hinc);
+}
+
+# This is a core logic of cigar string. The finite state machine theory is 
+# apply. See the below table, x-axis represents the input, with 3 options: 
+# (+/+) -- Both current query and subject bases are non-gap. Match
+# (-/+) -- The current query base is gap, but subject not. Deletion
+# (+/-) -- The current subject base is gap, but query not. Insertion
+# While the y-axis means the current state with letter 'M', 'D', 'I'
+#
+# The content of this table is the action taken in response of the input and 
+# the current state.
+# R     remain the state, counter increment.
+# G;X   generate the cigar line based on the current state and counter;
+#       clear the counter to zero and change to the state X
+#       
+#       ||  +/+  |  -/+ |  +/-  |
+# -------+----------------------+
+#    M  ||   R   |  G;D |   G;I |
+# ------------------------------+
+#    D  ||  G;M  |   R  |   G;I |
+# ------------------------------+   
+#    I  ||  G;M  |  G;D |    R  |
+#
+
+=head2 generate_cigar_string
+
+  Name : generate_cigar_string
+  Usage: $cigar_string = $self->generate_cigar_string(\@qchars, \@hchars);
+  Function: generate the cigar string for a piece of alignment.
+  Args:     2 array references. The lengths of 2 arrays are the same
+  Return:   a cigar string
+
+=cut
+
+# Developer's Note: The method is originally abstracted from the concept of 
+# cigar string. It only asks the essential information of 2 sequence characters
+# of the alignment, while the BlastWorn::split_HSP asks more unused information
+# for cigar string, which is useful to form align_coordinates. - Juguang
+
+my ($count, $state); # strictly only used in the following 2 subs
+
+sub generate_cigar_string {
+
+#   my ($self, $qstart, $hstart, $qinc, $hinc, $qchars_ref, $hchars_ref) = @_;
+
+    my ($self, $qchars_ref, $hchars_ref) = @_;
+    
+    my @qchars = @{$qchars_ref};
+    my @hchars = @{$hchars_ref};
+
+    unless(scalar(@qchars) == scalar(@hchars)){
+        $self->throw("two sequences are not equal in lengths");
+    }
+    
+    $count = 0;
+    $state = 'M';    # the current state of gaps, (M, D, I) 
+   
+    my $cigar_string = '';
+    for(my $i=0; $i <= $#qchars; $i++){
+        my $qchar = $qchars[$i];
+        my $hchar = $hchars[$i];
+        if($qchar ne '-' && $hchar ne '-'){ # Match
+            $cigar_string .= $self->_sub_cigar_string('M');
+        }elsif($qchar eq '-'){ # Deletion
+            $cigar_string .= $self->_sub_cigar_string('D');
+        }elsif($hchar eq '-'){ # Insertion
+            $cigar_string .= $self->_sub_cigar_string('I');
+        }else{
+            $self->throw("Impossible state that 2 gaps on each seq aligned");
+        }
+    }
+    $cigar_string .= $self->_sub_cigar_string('X'); # not forget the tail.
+    return $cigar_string;
+}
+
+sub _sub_cigar_string {
+    my ($self, $new_state) = @_;
+    my $sub_cigar_string = '';
+    if($state eq $new_state){
+        $count++; # Remain the state and increase the counter
+    }else{
+        $sub_cigar_string .= $count unless $count == 1;
+        $sub_cigar_string .= $state;
+        $count = 1;
+        $state = $new_state;
+    }
+    return $sub_cigar_string;
+}
+
+=head2 generate_cigar_string_by_hsp
+  
+  Name :    generate_cigar_string_by_hsp
+  Usage :   my $hsp; # a ready GenericHSP object
+my $cigar_string = $self->generate_cigar_string_by_hsp($hsp);
+  Function: generate a cigar string by given HSP object.
+  Args :    a GenericHSP object
+  Returns:  a text string of cigar string
+
+=cut
+
+sub generate_cigar_string_by_hsp {
+    my ($self, $hsp) = @_;
+
+    unless(ref($hsp) && $hsp->isa('Bio::Search::HSP::GenericHSP')){
+        $self->throw("A GenericHSP object needed");
+    }
+
+    my @qchars = split(//, $hsp->query_string);
+    my @hchars = split(//, $hsp->hit_string);
+
+    return $self->generate_cigar_string(\@qchars, \@hchars);
+}
+
+1;