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Commit 448cea7c authored by Alessandro Vullo's avatar Alessandro Vullo
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Added circular slice case for positive/negative strands when computing slice relative coordinates

parent 680bb69c
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Showing with 727 additions and 78 deletions
modules/Bio/EnsEMBL/DBSQL/AssemblyExceptionFeatureAdaptor.pm
View file @ 448cea7c
......@@ -324,14 +324,108 @@ sub _remap {
# create new copies of successfully mapped feaatures with shifted start,
# end and strand
my ($new_start, $new_end);
if($slice_strand == -1) {
$new_start = $slice_end - $end + 1;
$new_end = $slice_end - $start + 1;
} else {
$new_start = $start - $slice_start + 1;
$new_end = $end - $slice_start + 1;
}
# if($slice_strand == -1) {
# $new_start = $slice_end - $end + 1;
# $new_end = $slice_end - $start + 1;
# } else {
# $new_start = $start - $slice_start + 1;
# $new_end = $end - $slice_start + 1;
# }
my $seq_region_len = $slice->seq_region_length();
if ($slice_strand == 1) { # Positive strand
$new_start = $start - $slice_start + 1;
$new_end = $end - $slice_start + 1;
if ($slice->is_circular()) {
# Handle circular chromosomes.
if ($new_start > $new_end) {
# Looking at a feature overlapping the chromsome origin.
if ($new_end > $slice_start) {
# Looking at the region in the beginning of the
# chromosome.
$new_start -= $seq_region_len;
}
if ($new_end < 0) {
$new_end += $seq_region_len;
}
} else {
if ( $slice_start > $slice_end
&& $new_end < 0) {
# Looking at the region overlapping the chromosome
# origin and a feature which is at the beginning of the
# chromosome.
$new_start += $seq_region_len;
$new_end += $seq_region_len;
}
}
} ## end if ($dest_slice->is_circular...)
} else { # Negative strand
my $new_start = $slice_end - $end + 1;
my $new_end = $slice_end - $start + 1;
if ($slice->is_circular()) {
if ($slice_start > $slice_end) {
# slice spans origin or replication
if ($start >= $slice_start) {
$new_end += $seq_region_len;
$new_start += $seq_region_len
if $end > $slice_start;
} elsif ($start <= $slice_end) {
# do nothing
} elsif ($end >= $slice_start) {
$new_start += $seq_region_len;
$new_end += $seq_region_len;
} elsif ($end <= $slice_end) {
$new_end += $seq_region_len
if $new_end < 0;
} elsif ($start > $end) {
$new_end += $seq_region_len;
} else {
}
} else {
if ($start <= $slice_end and $end >= $slice_start) {
# do nothing
} elsif ($start > $end) {
if ($start <= $slice_end) {
$new_start -= $seq_region_len;
} elsif ($end >= $slice_start) {
$new_end += $seq_region_len;
} else {
}
}
}
}
} ## end else [ if ($dest_slice_strand...)]
push @out, Bio::EnsEMBL::AssemblyExceptionFeature->new(
'-dbID' => $f->dbID,
'-start' => $new_start,
......
modules/Bio/EnsEMBL/DBSQL/DnaAlignFeatureAdaptor.pm
View file @ 448cea7c
......@@ -501,25 +501,112 @@ FEATURE:
# If a destination slice was provided, convert the coords. If the
# dest_slice starts at 1 and is forward strand, nothing needs doing.
if ( defined($dest_slice) ) {
if ( $dest_slice_start != 1 || $dest_slice_strand != 1 ) {
if ( $dest_slice_strand == 1 ) {
$seq_region_start = $seq_region_start - $dest_slice_start + 1;
$seq_region_end = $seq_region_end - $dest_slice_start + 1;
} else {
my $tmp_seq_region_start = $seq_region_start;
$seq_region_start = $dest_slice_end - $seq_region_end + 1;
$seq_region_end = $dest_slice_end - $tmp_seq_region_start + 1;
$seq_region_strand = -$seq_region_strand;
}
my $seq_region_len = $dest_slice->seq_region_length();
if ($dest_slice_strand == 1) { # Positive strand
$seq_region_start = $seq_region_start - $dest_slice_start + 1;
$seq_region_end = $seq_region_end - $dest_slice_start + 1;
if ($dest_slice->is_circular()) {
# Handle cicular chromosomes.
if ($seq_region_start > $seq_region_end) {
# Looking at a feature overlapping the chromsome origin.
if ($seq_region_end > $dest_slice_start) {
# Looking at the region in the beginning of the
# chromosome.
$seq_region_start -= $seq_region_len;
}
if ($seq_region_end < 0) {
$seq_region_end += $seq_region_len;
}
} else {
if ( $dest_slice_start > $dest_slice_end
&& $seq_region_end < 0) {
# Looking at the region overlapping the chromosome
# origin and a feature which is at the beginning of the
# chromosome.
$seq_region_start += $seq_region_len;
$seq_region_end += $seq_region_len;
}
}
} ## end if ($dest_slice->is_circular...)
} else { # Negative strand
my $start = $dest_slice_end - $seq_region_end + 1;
my $end = $dest_slice_end - $seq_region_start + 1;
if ($dest_slice->is_circular()) {
if ($dest_slice_start > $dest_slice_end) {
# slice spans origin or replication
if ($seq_region_start >= $dest_slice_start) {
$end += $seq_region_len;
$start += $seq_region_len
if $seq_region_end > $dest_slice_start;
# Throw away features off the end of the requested slice.
if ( $seq_region_end < 1
|| $seq_region_start > $dest_slice_length
|| ( $dest_slice_seq_region_id ne $seq_region_id ) )
} elsif ($seq_region_start <= $dest_slice_end) {
# do nothing
} elsif ($seq_region_end >= $dest_slice_start) {
$start += $seq_region_len;
$end += $seq_region_len;
} elsif ($seq_region_end <= $dest_slice_end) {
$end += $seq_region_len
if $end < 0;
} elsif ($seq_region_start > $seq_region_end) {
$end += $seq_region_len;
} else {
}
} else {
if ($seq_region_start <= $dest_slice_end and $seq_region_end >= $dest_slice_start) {
# do nothing
} elsif ($seq_region_start > $seq_region_end) {
if ($seq_region_start <= $dest_slice_end) {
$start -= $seq_region_len;
} elsif ($seq_region_end >= $dest_slice_start) {
$end += $seq_region_len;
} else {
}
}
}
}
$seq_region_start = $start;
$seq_region_end = $end;
$seq_region_strand *= -1;
} ## end else [ if ($dest_slice_strand...)]
# Throw away features off the end of the requested slice.
if ( $seq_region_end < 1
|| $seq_region_start > $dest_slice_length
|| ( $dest_slice_seq_region_id ne $seq_region_id ) )
{
next FEATURE;
}
}
$slice = $dest_slice;
}
......
modules/Bio/EnsEMBL/DBSQL/MiscFeatureAdaptor.pm
View file @ 448cea7c
......@@ -469,20 +469,106 @@ sub _objs_from_sth {
#
# If a destination slice was provided convert the coords
# If the dest_slice starts at 1 and is foward strand, nothing needs doing
#
if ($dest_slice) {
if ($dest_slice_start != 1 || $dest_slice_strand != 1) {
if ($dest_slice_strand == 1) {
$seq_region_start = $seq_region_start - $dest_slice_start + 1;
$seq_region_end = $seq_region_end - $dest_slice_start + 1;
} else {
my $tmp_seq_region_start = $seq_region_start;
$seq_region_start = $dest_slice_end - $seq_region_end + 1;
$seq_region_end = $dest_slice_end - $tmp_seq_region_start + 1;
$seq_region_strand *= -1;
}
}
my $seq_region_len = $dest_slice->seq_region_length();
if ($dest_slice_strand == 1) { # Positive strand
$seq_region_start = $seq_region_start - $dest_slice_start + 1;
$seq_region_end = $seq_region_end - $dest_slice_start + 1;
if ($dest_slice->is_circular()) {
# Handle cicular chromosomes.
if ($seq_region_start > $seq_region_end) {
# Looking at a feature overlapping the chromsome origin.
if ($seq_region_end > $dest_slice_start) {
# Looking at the region in the beginning of the
# chromosome.
$seq_region_start -= $seq_region_len;
}
if ($seq_region_end < 0) {
$seq_region_end += $seq_region_len;
}
} else {
if ( $dest_slice_start > $dest_slice_end
&& $seq_region_end < 0) {
# Looking at the region overlapping the chromosome
# origin and a feature which is at the beginning of the
# chromosome.
$seq_region_start += $seq_region_len;
$seq_region_end += $seq_region_len;
}
}
} ## end if ($dest_slice->is_circular...)
} else { # Negative strand
my $start = $dest_slice_end - $seq_region_end + 1;
my $end = $dest_slice_end - $seq_region_start + 1;
if ($dest_slice->is_circular()) {
if ($dest_slice_start > $dest_slice_end) {
# slice spans origin or replication
if ($seq_region_start >= $dest_slice_start) {
$end += $seq_region_len;
$start += $seq_region_len
if $seq_region_end > $dest_slice_start;
} elsif ($seq_region_start <= $dest_slice_end) {
# do nothing
} elsif ($seq_region_end >= $dest_slice_start) {
$start += $seq_region_len;
$end += $seq_region_len;
} elsif ($seq_region_end <= $dest_slice_end) {
$end += $seq_region_len
if $end < 0;
} elsif ($seq_region_start > $seq_region_end) {
$end += $seq_region_len;
} else {
}
} else {
if ($seq_region_start <= $dest_slice_end and $seq_region_end >= $dest_slice_start) {
# do nothing
} elsif ($seq_region_start > $seq_region_end) {
if ($seq_region_start <= $dest_slice_end) {
$start -= $seq_region_len;
} elsif ($seq_region_end >= $dest_slice_start) {
$end += $seq_region_len;
} else {
}
}
}
}
$seq_region_start = $start;
$seq_region_end = $end;
$seq_region_strand *= -1;
} ## end else [ if ($dest_slice_strand...)]
#throw away features off the end of the requested slice
if ($seq_region_end < 1 || $seq_region_start > $dest_slice_length ||
( $dest_slice_sr_id ne $seq_region_id )) {
......@@ -490,6 +576,7 @@ sub _objs_from_sth {
$throw_away = $misc_feature_id;
next FEATURE;
}
$slice = $dest_slice;
}
......
modules/Bio/EnsEMBL/DBSQL/PredictionTranscriptAdaptor.pm
View file @ 448cea7c
......@@ -383,20 +383,105 @@ sub _objs_from_sth {
#
# If a destination slice was provided convert the coords
# If the dest_slice starts at 1 and is foward strand, nothing needs doing
#
if($dest_slice) {
if($dest_slice_start != 1 || $dest_slice_strand != 1) {
if($dest_slice_strand == 1) {
$seq_region_start = $seq_region_start - $dest_slice_start + 1;
$seq_region_end = $seq_region_end - $dest_slice_start + 1;
} else {
my $tmp_seq_region_start = $seq_region_start;
$seq_region_start = $dest_slice_end - $seq_region_end + 1;
$seq_region_end = $dest_slice_end - $tmp_seq_region_start + 1;
$seq_region_strand *= -1;
my $seq_region_len = $dest_slice->seq_region_length();
if ($dest_slice_strand == 1) { # Positive strand
$seq_region_start = $seq_region_start - $dest_slice_start + 1;
$seq_region_end = $seq_region_end - $dest_slice_start + 1;
if ($dest_slice->is_circular()) {
# Handle cicular chromosomes.
if ($seq_region_start > $seq_region_end) {
# Looking at a feature overlapping the chromsome origin.
if ($seq_region_end > $dest_slice_start) {
# Looking at the region in the beginning of the
# chromosome.
$seq_region_start -= $seq_region_len;
}
if ($seq_region_end < 0) {
$seq_region_end += $seq_region_len;
}
} else {
if ( $dest_slice_start > $dest_slice_end
&& $seq_region_end < 0) {
# Looking at the region overlapping the chromosome
# origin and a feature which is at the beginning of the
# chromosome.
$seq_region_start += $seq_region_len;
$seq_region_end += $seq_region_len;
}
}
} ## end if ($dest_slice->is_circular...)
} else { # Negative strand
my $start = $dest_slice_end - $seq_region_end + 1;
my $end = $dest_slice_end - $seq_region_start + 1;
if ($dest_slice->is_circular()) {
if ($dest_slice_start > $dest_slice_end) {
# slice spans origin or replication
if ($seq_region_start >= $dest_slice_start) {
$end += $seq_region_len;
$start += $seq_region_len
if $seq_region_end > $dest_slice_start;
} elsif ($seq_region_start <= $dest_slice_end) {
# do nothing
} elsif ($seq_region_end >= $dest_slice_start) {
$start += $seq_region_len;
$end += $seq_region_len;
} elsif ($seq_region_end <= $dest_slice_end) {
$end += $seq_region_len
if $end < 0;
} elsif ($seq_region_start > $seq_region_end) {
$end += $seq_region_len;
} else {
}
} else {
if ($seq_region_start <= $dest_slice_end and $seq_region_end >= $dest_slice_start) {
# do nothing
} elsif ($seq_region_start > $seq_region_end) {
if ($seq_region_start <= $dest_slice_end) {
$start -= $seq_region_len;
} elsif ($seq_region_end >= $dest_slice_start) {
$end += $seq_region_len;
} else {
}
}
}
}
}
$seq_region_start = $start;
$seq_region_end = $end;
$seq_region_strand *= -1;
} ## end else [ if ($dest_slice_strand...)]
#throw away features off the end of the requested slice
if($seq_region_end < 1 || $seq_region_start > $dest_slice_length ||
......@@ -404,7 +489,6 @@ sub _objs_from_sth {
next FEATURE;
}
$slice = $dest_slice;
}
......
modules/Bio/EnsEMBL/DBSQL/ProteinAlignFeatureAdaptor.pm
View file @ 448cea7c
......@@ -287,26 +287,112 @@ sub _objs_from_sth {
#
# If a destination slice was provided convert the coords
# If the dest_slice starts at 1 and is foward strand, nothing needs doing
#
if($dest_slice) {
if($dest_slice_start != 1 || $dest_slice_strand != 1) {
if($dest_slice_strand == 1) {
$seq_region_start = $seq_region_start - $dest_slice_start + 1;
$seq_region_end = $seq_region_end - $dest_slice_start + 1;
} else {
my $tmp_seq_region_start = $seq_region_start;
$seq_region_start = $dest_slice_end - $seq_region_end + 1;
$seq_region_end = $dest_slice_end - $tmp_seq_region_start + 1;
$seq_region_strand *= -1;
}
}
my $seq_region_len = $dest_slice->seq_region_length();
if ($dest_slice_strand == 1) { # Positive strand
$seq_region_start = $seq_region_start - $dest_slice_start + 1;
$seq_region_end = $seq_region_end - $dest_slice_start + 1;
if ($dest_slice->is_circular()) {
# Handle cicular chromosomes.
if ($seq_region_start > $seq_region_end) {
# Looking at a feature overlapping the chromsome origin.
if ($seq_region_end > $dest_slice_start) {
# Looking at the region in the beginning of the
# chromosome.
$seq_region_start -= $seq_region_len;
}
if ($seq_region_end < 0) {
$seq_region_end += $seq_region_len;
}
} else {
if ( $dest_slice_start > $dest_slice_end
&& $seq_region_end < 0) {
# Looking at the region overlapping the chromosome
# origin and a feature which is at the beginning of the
# chromosome.
$seq_region_start += $seq_region_len;
$seq_region_end += $seq_region_len;
}
}
} ## end if ($dest_slice->is_circular...)
} else { # Negative strand
my $start = $dest_slice_end - $seq_region_end + 1;
my $end = $dest_slice_end - $seq_region_start + 1;
if ($dest_slice->is_circular()) {
if ($dest_slice_start > $dest_slice_end) {
# slice spans origin or replication
if ($seq_region_start >= $dest_slice_start) {
$end += $seq_region_len;
$start += $seq_region_len
if $seq_region_end > $dest_slice_start;
} elsif ($seq_region_start <= $dest_slice_end) {
# do nothing
} elsif ($seq_region_end >= $dest_slice_start) {
$start += $seq_region_len;
$end += $seq_region_len;
} elsif ($seq_region_end <= $dest_slice_end) {
$end += $seq_region_len
if $end < 0;
} elsif ($seq_region_start > $seq_region_end) {
$end += $seq_region_len;
} else {
}
} else {
if ($seq_region_start <= $dest_slice_end and $seq_region_end >= $dest_slice_start) {
# do nothing
} elsif ($seq_region_start > $seq_region_end) {
if ($seq_region_start <= $dest_slice_end) {
$start -= $seq_region_len;
} elsif ($seq_region_end >= $dest_slice_start) {
$end += $seq_region_len;