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Commit ddf36962 authored by Arne Stabenau's avatar Arne Stabenau
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BaseAlignFeature split on contig boundary now looses split codon alignment

parent e7fec65c
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Showing with 77 additions and 229 deletions
modules/Bio/EnsEMBL/BaseAlignFeature.pm
View file @ ddf36962
......@@ -911,6 +911,7 @@ sub _transform_feature_to_RawContig{
my @out;
my ( $hit_start, $hit_end );
my $codon_unused_bases = 0;
if( scalar( @mapped ) > 1 ) {
#The feature needs to be mapped accross multiple contigs
......@@ -931,14 +932,58 @@ sub _transform_feature_to_RawContig{
#caculate query and hit length for each portion of the split feature
#may need to round hit length to avoid 'partial' peptide
# decision of Michele to not cover split codons
my $query_length = ($mapped[$i]->end - $mapped[$i]->start + 1);
my $query_start = $mapped[$i]->start();
my $query_end = $mapped[$i]->end();
my $hit_length;
if($self->_query_unit == $self->_hit_unit){
# DnaDna and PepPep case
$hit_length = $query_length;
}elsif($self->_query_unit > $self->_hit_unit){
my $tmp = ($query_length/$self->_query_unit);
$hit_length = sprintf "%.0f", $tmp; #round value up or down
}elsif($self->_hit_unit > $self->_query_unit){
} elsif( $self->_query_unit > $self->_hit_unit ){
# DnaPepAlign case
# my $tmp = ($query_length/$self->_query_unit);
# $hit_length = sprintf "%.0f", $tmp; #round value up or down
$hit_length = int(( $query_length - $codon_unused_bases ) /
$self->_query_unit() );
if( $codon_unused_bases ) {
if( $feature->hstrand() == 1 ) {
$hit_start++;
} else {
$hit_end--;
}
}
my $used_bases = $query_length - $codon_unused_bases -
$hit_length*$self->_query_unit();
if( $mapped[$i]->strand() == -1 ) {
$query_end -= $codon_unused_bases;
$query_start += $used_bases;
} else {
$query_start += $codon_unused_bases;
$query_end -= $used_bases;
}
# new rest at the end ...
if( $used_bases ) {
$codon_unused_bases = 3 - $used_bases;
} else {
$codon_unused_bases = 0;
}
} elsif($self->_hit_unit > $self->_query_unit){
# PepDnaAlign case (rare)
my $tmp = ($query_length*$self->_hit_unit);
$hit_length = sprintf "%.0f", $tmp; #round value up or down
}
......@@ -946,6 +991,7 @@ sub _transform_feature_to_RawContig{
if($hit_length == 0){
next SPLIT;
}
if( $feature->hstrand() == 1 ) {
$hit_end = ($hit_start + $hit_length) - 1;
} else {
......@@ -957,8 +1003,8 @@ sub _transform_feature_to_RawContig{
#create the new feature
my $new_feature = Bio::EnsEMBL::FeaturePair->new;
$new_feature->start($mapped[$i]->start);
$new_feature->end($mapped[$i]->end);
$new_feature->start($query_start);
$new_feature->end($query_end);
$new_feature->strand($mapped[$i]->strand);
$new_feature->score($feature->score);
$new_feature->percent_id($feature->percent_id);
......
modules/Bio/EnsEMBL/Root.pm
View file @ ddf36962
......@@ -95,6 +95,8 @@ sub warn{
my ($self,$string) = @_;
my $verbose = $self->verbose;
$verbose = 0 unless defined $verbose;
if( $verbose == 2 ) {
$self->throw($string);
......
modules/t/dnaPepAlignFeature.t
View file @ ddf36962
......@@ -3,7 +3,7 @@ use lib 't';
BEGIN { $| = 1;
use Test;
plan tests => 63;
plan tests => 39;
}
use MultiTestDB;
......@@ -11,6 +11,11 @@ use Bio::EnsEMBL::DnaPepAlignFeature;
use Bio::EnsEMBL::SeqFeature;
use Bio::EnsEMBL::RawContig;
use TestUtils qw ( debug test_getter_setter );
# switch on the debug prints
our $verbose = 0;
my($CHR, $START, $END) = ('20', 30_363_615, 30_475_000);
my $CTG_BOUNDARY = 62877;
......@@ -143,12 +148,12 @@ ok($f);
#
@feats = ();
$fp = new Bio::EnsEMBL::FeaturePair;
$fp->start($CTG_BOUNDARY - 2);
$fp->end ($CTG_BOUNDARY);
$fp->start($CTG_BOUNDARY - 5);
$fp->end ($CTG_BOUNDARY );
$fp->strand(1);
$fp->score(10);
$fp->contig($slice);
$fp->hstart(105);
$fp->hstart(104);
$fp->hend (105);
$fp->hstrand (1);
$fp->hseqname('dummy-hid');
......@@ -180,7 +185,7 @@ push(@feats,$fp);
$dnaf = Bio::EnsEMBL::DnaPepAlignFeature->new( -features => \@feats );
ok($dnaf);
ok($dnaf->cigar_string eq '3M3I6M6D3M');
ok($dnaf->cigar_string eq '6M3I6M6D3M');
ok($dnaf->validate || 1); #validate doesn't return true but throws on fail
@dnafs = $dnaf->transform;
......@@ -189,63 +194,10 @@ ok($dnafs[0]->validate || 1);
ok($dnafs[1]->validate || 1);
#
# 22-27 create a dnaalign feature on a slice across a contig boundary
# and convert to raw contig coordinates
# (+ve strand, -ve hitstrand)
#
@feats = ();
$fp = new Bio::EnsEMBL::FeaturePair;
$fp->start($CTG_BOUNDARY - 2);
$fp->end ($CTG_BOUNDARY);
$fp->strand(1);
$fp->score(10);
$fp->contig($slice);
$fp->hstart (108);
$fp->hend (108);
$fp->hstrand (-1);
$fp->hseqname('dummy-hid');
push(@feats,$fp);
$fp = new Bio::EnsEMBL::FeaturePair;
$fp->start($CTG_BOUNDARY + 4);
$fp->end ($CTG_BOUNDARY + 9);
$fp->strand(1);
$fp->score(10);
$fp->contig($slice);
$fp->seqname(1);
$fp->hstart(106);
$fp->hend (107);
$fp->hstrand (-1);
$fp->hseqname('dummy-hid');
push(@feats,$fp);
$fp = new Bio::EnsEMBL::FeaturePair;
$fp->start($CTG_BOUNDARY + 10);
$fp->end ($CTG_BOUNDARY + 12);
$fp->strand(1);
$fp->score(10);
$fp->contig($slice);
$fp->hstart (103);
$fp->hend (103);
$fp->hstrand (-1);
$fp->hseqname('dummy-hid');
push(@feats,$fp);
$dnaf = Bio::EnsEMBL::DnaPepAlignFeature->new( -features => \@feats );
ok($dnaf);
ok($dnaf->cigar_string eq '3M3I6M6D3M');
ok($dnaf->validate || 1); #validate doesn't return true but throws on fail
my @dnafs = $dnaf->transform;
ok(scalar(@dnafs) == 2);
ok($dnafs[0]->validate || 1);
ok($dnafs[1]->validate || 1);
#
# 28-33 create a dnaalign feature on a slice across a contig boundary
# 22-27 create a dnaalign feature on a slice across a contig boundary
# and convert to raw contig coordinates
# (-ve strand, +ve hitstrand)
#
......@@ -296,65 +248,21 @@ ok($dnaf->validate || 1); #validate doesn't return true but throws on fail
@dnafs = $dnaf->transform;
ok(scalar(@dnafs) == 2);
ok($dnafs[0]->validate || 1);
ok($dnafs[1]->validate || 1);
#
# 34-39 create a dnaalign feature on a slice across a contig boundary
# and convert to raw contig coordinates
# (-ve strand, -ve hitstrand)
#
@feats = ();
$fp = new Bio::EnsEMBL::FeaturePair;
$fp->start($CTG_BOUNDARY + 3);
$fp->end ($CTG_BOUNDARY + 5);
$fp->strand(-1);
$fp->score(10);
$fp->contig($slice);
$fp->hstart (108);
$fp->hend (108);
$fp->hstrand (-1);
$fp->hseqname('dummy-hid');
push(@feats,$fp);
$fp = new Bio::EnsEMBL::FeaturePair;
$fp->start($CTG_BOUNDARY - 6);
$fp->end ($CTG_BOUNDARY - 1);
$fp->strand(-1);
$fp->score(10);
$fp->contig($slice);
$fp->seqname(1);
$fp->hstart(106);
$fp->hend (107);
$fp->hstrand (-1);
$fp->hseqname('dummy-hid');
push(@feats,$fp);
debug( "Feature 0 dump" );
while( my ($k, $v) = each %{$dnafs[0]} ) {
debug( " ->".$k." = ".$v );
}
ok($dnafs[0]->validate || 1);
$fp = new Bio::EnsEMBL::FeaturePair;
$fp->start($CTG_BOUNDARY - 9);
$fp->end ($CTG_BOUNDARY - 7);
$fp->strand(-1);
$fp->score(10);
$fp->contig($slice);
$fp->seqname(1);
$fp->hstart(103);
$fp->hend(103);
$fp->hstrand (-1);
$fp->hseqname('dummy-hid');
push(@feats,$fp);
debug( "Feature 1 dump" );
while( my ($k, $v) = each %{$dnafs[1]} ) {
debug( " ->".$k." = ".$v );
}
ok($dnafs[1]->validate || 1);
$dnaf = Bio::EnsEMBL::DnaPepAlignFeature->new( -features => \@feats );
ok($dnaf);
ok($dnaf->cigar_string eq '3M3I6M6D3M');
ok($dnaf->validate || 1); #validate doesn't return true but throws on fail
@dnafs = $dnaf->transform;
ok(scalar(@dnafs) == 2);
ok($dnafs[0]->validate || 1);
ok($dnafs[1]->validate || 1);
#
......@@ -368,7 +276,7 @@ $slice = $slice->invert;
#
# 40-45 create a dnaalign feature on a slice across a contig boundary
# 28-33 create a dnaalign feature on a slice across a contig boundary
# and convert to raw contig coordinates
# (+ve strand, +ve hitstrand)
#
......@@ -420,63 +328,9 @@ ok($dnafs[0]->validate || 1);
ok($dnafs[1]->validate || 1);
#
# 46-51 create a dnaalign feature on a slice across a contig boundary
# and convert to raw contig coordinates
# (+ve strand, -ve hitstrand)
#
@feats = ();
$fp = new Bio::EnsEMBL::FeaturePair;
$fp->start($CTG_BOUNDARY - 2);
$fp->end ($CTG_BOUNDARY);
$fp->strand(1);
$fp->score(10);
$fp->contig($slice);
$fp->hstart (108);
$fp->hend (108);
$fp->hstrand (-1);
$fp->hseqname('dummy-hid');
push(@feats,$fp);
$fp = new Bio::EnsEMBL::FeaturePair;
$fp->start($CTG_BOUNDARY + 4);
$fp->end ($CTG_BOUNDARY + 9);
$fp->strand(1);
$fp->score(10);
$fp->contig($slice);
$fp->seqname(1);
$fp->hstart(106);
$fp->hend (107);
$fp->hstrand (-1);
$fp->hseqname('dummy-hid');
push(@feats,$fp);
$fp = new Bio::EnsEMBL::FeaturePair;
$fp->start($CTG_BOUNDARY + 10);
$fp->end ($CTG_BOUNDARY + 12);
$fp->strand(1);
$fp->score(10);
$fp->contig($slice);
$fp->hstart (103);
$fp->hend (103);
$fp->hstrand (-1);
$fp->hseqname('dummy-hid');
push(@feats,$fp);
$dnaf = Bio::EnsEMBL::DnaPepAlignFeature->new( -features => \@feats );
ok($dnaf);
ok($dnaf->cigar_string eq '3M3I6M6D3M');
ok($dnaf->validate || 1); #validate doesn't return true but throws on fail
@dnafs = $dnaf->transform;
ok(scalar(@dnafs) == 2);
ok($dnafs[0]->validate || 1);
ok($dnafs[1]->validate || 1);
#
# 52-57 create a dnaalign feature on a slice across a contig boundary
# 34-39 create a dnaalign feature on a slice across a contig boundary
# and convert to raw contig coordinates
# (-ve strand, +ve hitstrand)
#
......@@ -532,57 +386,3 @@ ok($dnafs[1]->validate || 1);
#
# 58-63 create a dnaalign feature on a slice across a contig boundary
# and convert to raw contig coordinates
# (-ve strand, -ve hitstrand)
#
@feats = ();
$fp = new Bio::EnsEMBL::FeaturePair;
$fp->start($CTG_BOUNDARY + 3);
$fp->end ($CTG_BOUNDARY + 5);
$fp->strand(-1);
$fp->score(10);
$fp->contig($slice);
$fp->hstart (108);
$fp->hend (108);
$fp->hstrand (-1);
$fp->hseqname('dummy-hid');
push(@feats,$fp);
$fp = new Bio::EnsEMBL::FeaturePair;
$fp->start($CTG_BOUNDARY - 6);
$fp->end ($CTG_BOUNDARY - 1);
$fp->strand(-1);
$fp->score(10);
$fp->contig($slice);
$fp->seqname(1);
$fp->hstart(106);
$fp->hend (107);
$fp->hstrand (-1);
$fp->hseqname('dummy-hid');
push(@feats,$fp);
$fp = new Bio::EnsEMBL::FeaturePair;
$fp->start($CTG_BOUNDARY - 9);
$fp->end ($CTG_BOUNDARY - 7);
$fp->strand(-1);
$fp->score(10);
$fp->contig($slice);
$fp->seqname(1);
$fp->hstart(103);
$fp->hend(103);
$fp->hstrand (-1);
$fp->hseqname('dummy-hid');
push(@feats,$fp);
$dnaf = Bio::EnsEMBL::DnaPepAlignFeature->new( -features => \@feats );
ok($dnaf);
ok($dnaf->cigar_string eq '3M3I6M6D3M');
ok($dnaf->validate || 1); #validate doesn't return true but throws on fail
@dnafs = $dnaf->transform;
ok(scalar(@dnafs) == 2);
ok($dnafs[0]->validate || 1);
ok($dnafs[1]->validate || 1);
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