From f3625fc9fb7cd53a6c353c148beac7d535567261 Mon Sep 17 00:00:00 2001
From: Ewan Birney <birney@sanger.ac.uk>
Date: Tue, 25 Apr 2000 09:02:42 +0000
Subject: [PATCH] delt with left and right overhang possibilities.
checked lengths. Look good.
---
modules/Bio/EnsEMBL/DB/VirtualContig.pm | 176 +++++++++++++++++++-----
1 file changed, 142 insertions(+), 34 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DB/VirtualContig.pm b/modules/Bio/EnsEMBL/DB/VirtualContig.pm
index 2884c81320..104109d1e5 100755
--- a/modules/Bio/EnsEMBL/DB/VirtualContig.pm
+++ b/modules/Bio/EnsEMBL/DB/VirtualContig.pm
@@ -109,6 +109,9 @@ sub _initialize {
# this is for cache's of sequence features if/when we want them
$self->{'_sf_cache'} = {};
+ $self->_left_overhang(0);
+ $self->_right_overhang(0);
+
if( defined $clone && defined $focuscontig ){
$self->throw("Build a virtual contig either with a clone or a focuscontig, but not with both");
}
@@ -284,10 +287,14 @@ sub windowed_VirtualContig {
my @ids = keys %{$self->{'contighash'}};
@ids = sort { $self->{'start'}->{$b} <=> $self->{'start'}->{$a} } @ids;
+ print STDERR "In Windowed vc...\n";
+
print STDERR @ids."\n\n";
my $id = undef;
- foreach ( @ids ) {
+ foreach $_ ( @ids ) {
+ print STDERR "Looking at $_\n";
+
if( $self->start_in_vc($_) < $position ) {
print STDERR "Starting contig: $_ [". $self->start_in_vc($_). " < $position] \n";
$id = $_;
@@ -350,6 +357,12 @@ sub primary_seq {
my $seq_string;
my $last_point = 1;
+ # if there is a left overhang, add it
+
+ if( $self->_left_overhang() > 0 ) {
+ $seq_string = 'N' x $self->_left_overhang();
+ }
+
foreach my $cid ( @contig_id ) {
#print(STDERR "\nFinding sequence for $cid\n");
my $c = $self->{'contighash'}->{$cid};
@@ -407,6 +420,13 @@ sub primary_seq {
$last_point += length($trunc);
}
+ # if there is a right overhang, add it
+
+ if( $self->_right_overhang() > 0 ) {
+ $seq_string .= 'N' x $self->_right_overhang();
+ }
+
+
$seq = Bio::PrimarySeq->new( -id => "virtual_contig_".$self->_unique_number,
-seq => $seq_string,
-moltype => 'dna'
@@ -867,6 +887,8 @@ sub _build_contig_map {
print STDERR "Left size is $left\n";
+ GOING_LEFT :
+
while( $current_left_size < $left ) {
print(STDERR "Current left = $current_left_size\n");
print STDERR "Looking at ",$current_contig->id," with $current_left_size\n";
@@ -894,6 +916,12 @@ sub _build_contig_map {
$current_left_size += $overlap->sister->golden_length -1;
} else {
$current_left_size += $overlap->distance;
+ if( $current_left_size > $left ) {
+ # set the left overhang!
+ print STDERR "Triggered left overhang - ",$overlap->distance,":$current_left_size\n";
+ $self->_left_overhang($overlap->distance - ($current_left_size - $left));
+ last GOING_LEFT;
+ }
$current_left_size += $overlap->sister->golden_length;
}
@@ -921,6 +949,11 @@ sub _build_contig_map {
$current_left_size += $overlap->sister->golden_length-1;
} else {
$current_left_size += $overlap->distance;
+ if( $current_left_size < $left ) {
+ # set the left overhang!
+ $self->_left_overhang($overlap->distance - ($current_left_size - $left));
+ last GOING_LEFT;
+ }
$current_left_size += $overlap->sister->golden_length;
}
@@ -948,38 +981,53 @@ sub _build_contig_map {
my $startpos;
-
- print STDERR "Leftmost contig starts at: $startpos orientation: $current_orientation\n";
- print STDERR "Current left = $left vs global left= $current_left_size\n";
-
- if( $current_orientation == 1 ) {
- print(STDERR "Current orientation $current_orientation\n");
- print(STDERR "golden start " . $current_contig->golden_start . "\n");
- $startpos = $current_contig->golden_start + ($current_left_size - $left);
- } else {
- print(STDERR "Current orientation $current_orientation\n");
- print(STDERR "golden end " . $current_contig->golden_end . "\n");
-
- $startpos = $current_contig->golden_end - ($current_left_size - $left);
- }
- print STDERR "Leftmost contig has $startpos and $current_orientation $left vs $current_left_size\n";
+ print STDERR "Leftmost contig starts at: $startpos orientation: $current_orientation\n";
+ print STDERR "Current left = $left vs global left= $current_left_size\n";
- $self->{'start'} ->{$current_contig->id} = 1;
- $self->{'startincontig'}->{$current_contig->id} = $startpos;
- $self->{'contigori'} ->{$current_contig->id} = $current_orientation;
- $self->{'contighash'} ->{$current_contig->id} = $current_contig;
-
-
- my $current_length;
- if( $current_orientation == 1 ) {
- # mystic +1 due to biological counting scheme
- $current_length = $current_contig->golden_end - $startpos +1;
+ my $current_length;
+
+ if( $self->_left_overhang() == 0 ) {
+ if( $current_orientation == 1 ) {
+ print(STDERR "Current orientation $current_orientation\n");
+ print(STDERR "golden start " . $current_contig->golden_start . "\n");
+ $startpos = $current_contig->golden_start + ($current_left_size - $left);
+ } else {
+ print(STDERR "Current orientation $current_orientation\n");
+ print(STDERR "golden end " . $current_contig->golden_end . "\n");
+
+ $startpos = $current_contig->golden_end - ($current_left_size - $left);
+ }
+
+ print STDERR "Leftmost contig has $startpos and $current_orientation $left vs $current_left_size\n";
+
+ $self->{'start'} ->{$current_contig->id} = 1;
+ $self->{'startincontig'}->{$current_contig->id} = $startpos;
+ $self->{'contigori'} ->{$current_contig->id} = $current_orientation;
+ $self->{'contighash'} ->{$current_contig->id} = $current_contig;
+
+ if( $current_orientation == 1 ) {
+ # mystic +1 due to biological counting scheme
+ $current_length = $current_contig->golden_end - $startpos +1;
+ } else {
+ # mystic +1 due to biological counting scheme
+ $current_length = $startpos - $current_contig->golden_start+1;
+ }
} else {
- # mystic +1 due to biological counting scheme
- $current_length = $startpos - $current_contig->golden_start+1;
+ # has an overhang - first contig offset into the system
+ $self->{'start'} ->{$current_contig->id} = $self->_left_overhang+1;
+ if( $current_orientation == 1 ) {
+ $self->{'startincontig'}->{$current_contig->id} = $current_contig->golden_start;
+ } else {
+ $self->{'startincontig'}->{$current_contig->id} = $current_contig->golden_end;
+ }
+ $self->{'contigori'} ->{$current_contig->id} = $current_orientation;
+ $self->{'contighash'} ->{$current_contig->id} = $current_contig;
+ $current_length = $self->_left_overhang() + $current_contig->golden_length;
}
+
+
print STDERR "current length before we get into this is $current_length\n";
while( $current_length < $total ) {
@@ -1002,6 +1050,14 @@ sub _build_contig_map {
last;
}
+ # see whether the distance gives us an end condition, and a right_overhang
+
+ if( $current_length + $overlap->distance > $total ) {
+ # right overhang
+ $self->_right_overhang($total - $current_length);
+ last;
+ }
+
# add to total, move on the contigs
$current_contig = $overlap->sister();
@@ -1097,12 +1153,20 @@ sub _build_contig_map {
# need to store end point for last contig
print STDERR "Looking at setting rightmost end with $total and $current_length ",$current_contig->golden_end,"\n";
- $self->{'rightmostcontig_id'} = $current_contig->id();
- if( $current_orientation == 1 ) {
- $self->{'rightmostend'} = $current_contig->golden_end - ($current_length - $total);
- } else {
- $self->{'rightmostend'} = $current_contig->golden_start + ($current_length - $total);
- }
+ $self->{'rightmostcontig_id'} = $current_contig->id();
+ if( $self->_right_overhang == 0 ) {
+ if( $current_orientation == 1 ) {
+ $self->{'rightmostend'} = $current_contig->golden_end - ($current_length - $total);
+ } else {
+ $self->{'rightmostend'} = $current_contig->golden_start + ($current_length - $total);
+ }
+ } else {
+ if( $current_orientation == 1 ) {
+ $self->{'rightmostend'} = $current_contig->golden_end;
+ } else {
+ $self->{'rightmostend'} = $current_contig->golden_start;
+ }
+ }
# put away the focus/size info etc
@@ -1711,6 +1775,50 @@ sub _at_right_end {
return $obj->{'_at_right_end'};
}
+
+=head2 _left_overhang
+
+ Title : _left_overhang
+ Usage : $obj->_left_overhang($newval)
+ Function:
+ Example :
+ Returns : value of _left_overhang
+ Args : newvalue (optional)
+
+
+=cut
+
+sub _left_overhang{
+ my ($obj,$value) = @_;
+ if( defined $value) {
+ $obj->{'_left_overhang'} = $value;
+ }
+ return $obj->{'_left_overhang'};
+
+}
+
+=head2 _right_overhang
+
+ Title : _right_overhang
+ Usage : $obj->_right_overhang($newval)
+ Function:
+ Example :
+ Returns : value of _right_overhang
+ Args : newvalue (optional)
+
+
+=cut
+
+sub _right_overhang{
+ my ($obj,$value) = @_;
+ if( defined $value) {
+ $obj->{'_right_overhang'} = $value;
+ }
+ return $obj->{'_right_overhang'};
+
+}
+
+
1;
--
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