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Commit f3625fc9 authored by Ewan Birney's avatar Ewan Birney
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delt with left and right overhang possibilities. 

checked lengths. Look good.
parent cadda367
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modules/Bio/EnsEMBL/DB/VirtualContig.pm
+ 142
− 34
View file @ f3625fc9
......@@ -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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