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Convert.nucmer_coord2block_bed.pl.bak
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Convert.nucmer_coord2block_bed.pl.bak
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#! perl
use warnings;
use strict;
use File::Basename;
use Getopt::Long;
use List::Util qw/max min/;
my($min,$gap,$prior,$gap2,$type);
GetOptions(
'prior=s' => \$prior,
'exgap=s' => \$gap,
'idgap=s' => \$gap2,
'min=s' => \$min,
'type=s' => \$type
);
my $file = shift;
if(!$file){
print STDERR "Usage : perl $0 \$coord_file [-type [r,q or 1,not support m] --min 0 --exgap 20000 --idgap 5000 --prior {muti line file, format:(sp1_chr1 sp2_chr2)} ]\n";
exit;
}
$min //= 0;$gap //= 20000;$gap2 //= 5000;$type //= "r";
(my $prefix = basename $file) =~ s/(.*)\..*/$1/;
my $o = $prefix.".block.bed";
my $extend = $gap/2;
my %p;
if($prior){
%p = &load_prior($prior);
}
my %h = &load_coord($file);
#[$l[9],$l[0],$l[1],$l[10],$l[2],$l[3],$direct,$l[7]];
open O,'>',$o;
for my $k(sort {$a cmp $b} keys %h){
my %o;
my $r_start;my $r_end;my $q_start;my $q_end;
my @data = sort{$a->[1]<=>$b->[1]} @{$h{$k}};
#print join"," ,@data;print "\n";
#next;
my $last = ${$data[0]}[6];;
my $jud = 1;
Do:for(my $i = 0; $i< @data;$i +=1){
my @l = @{$data[$i]};
#print join"\t",@l,"\n";next;
$l[1] -= $extend;
$l[4] -= $extend;
$l[2] += $extend;
$l[5] += $extend;
if($i > 0 && $jud == 1){
if($l[6] ne $last){
$o{$i} = \@l;
$last = $l[6];
$jud = 2;
next Do;
}
$q_start = $l[1];
$q_end = $l[2];
$r_start = $l[4];
$r_end = $l[5];
if($l[6] > 0){
if($r_end <= ${$o{$i-1}}[5]){
$o{$i} = \@l;
}elsif($q_start > ${$o{$i-1}}[2] && $r_start > ${$o{$i-1}}[5]){
$o{$i} = \@l;
}else{
my $q_interval = $q_start - ${$o{$i-1}}[2];
my $r_interval = $r_start - ${$o{$i-1}}[5];
if($q_interval >$gap2 || $r_interval > $gap2){
$o{$i} = \@l;
}else{
$o{$i} = $o{$i-1};
${$o{$i}}[2] = $q_end;
${$o{$i}}[5] = $r_end;
delete $o{$i-1};
}
}
}else{
if($r_start >= ${$o{$i-1}}[4]){
$o{$i} = \@l;
}elsif($q_start > ${$o{$i-1}}[2] && $r_end < ${$o{$i-1}}[4]){
$o{$i} = \@l;
}else{
my $q_interval = $q_start - ${$o{$i-1}}[2];
my $r_interval = ${$o{$i-1}}[4] - $r_end;
#print $q_interval.",".$r_interval;exit;
if($q_interval >$gap2 || $r_interval > $gap2){
$o{$i} = \@l;
}else{
$o{$i} = $o{$i-1};
${$o{$i}}[2] = $q_end;
${$o{$i}}[4] = $r_start;
delete $o{$i-1};
}
}
}
}else{
$o{$i} = \@l;
$last = $l[6];
$jud = 1;
}
}
for my $k (sort {$a <=> $b} keys %o){
my @t = @{$o{$k}};
$t[2] -= $extend;
$t[1] += $extend;
$t[5] -= $extend;
$t[4] += $extend;
push @t,$t[2] - $t[1];
push @t,$t[5] - $t[4];
my $p = join"\t",@t;
print O $p."\n";
}
}
sub coord_filter{
my $ref = shift @_;
my %h = %{$ref};
my @a = sort{$a cmp $b} keys %h;
my $c = 0;
for(my $i1 = 0;$i1 < @a;$i1+=1){
$c += 1;
next if (!exists $h{$a[$i1]});
my @l1 = @{$h{$a[$i1]}};
my $d1 = $l1[2] - $l1[1];
for(my $i2 = $c;$i2 < @a;$i2 += 1){
next if (!exists $h{$a[$i2]});
my @l2 = @{$h{$a[$i2]}};
next if $l1[0] ne $l2[0];
if($l1[2] >= $l2[1] && $l2[2] >= $l1[1]){
#print "$i1:$i2:$c#";
#print join",",@l1,"#";
#print join",",@l2,"\n";
#print "???";exit;
my $d2 = $l2[2] - $l2[1];
if($d1 > $d2){
delete $h{$a[$i2]};
}elsif($d1 == $d2){
if($l1[7] >= $l2[7]){
delete $h{$a[$i2]};
}else{
delete $h{$a[$i1]};
}
}elsif($d1 < $d2){
delete $h{$a[$i1]};
$d1 = $d2;
}
}
}
}
#print scalar keys %h;exit;
my %o;
if($type eq "r"){
for my $k (%h){
next if ! exists $h{$k};
my @t = @{$h{$k}};
@t = ($t[3],$t[4],$t[5],$t[0],$t[1],$t[2],$t[6],$t[7]);
@{$o{$k}} = @t;
}
}else{
for my $k (%h){
next if ! exists $h{$k};
@{$o{$k}} = @{$h{$k}};
}
}
return %o;
}
sub load_coord{
my $f = shift @_;
open IN,'<',$f;
my %h;
my %t;
while(<IN>){
next unless /^\d+/;
chomp;
my @l = split/\s+/;
if($prior){
next unless exists $p{"$l[9]-$l[10]"};
next unless exists $p{"$l[10]-$l[9]"};
}
next if $l[4] < $min;
next if $l[5] < $min;
my $direct = $l[7] * $l[8];
die "????" if $l[0] > $l[1];
if($l[2] > $l[3]){
my $tmp = $l[2];
$l[2] = $l[3];
$l[3] = $tmp;
}
if($type eq "r"){
$t{"$l[9]-$l[0]-$l[1]"} = [$l[10],$l[2],$l[3],$l[9],$l[0],$l[1],$direct,$l[6]];
}elsif($type eq "q"){
$t{"$l[10]-$l[2]-$l[3]"} = [$l[9],$l[0],$l[1],$l[10],$l[2],$l[3],$direct,$l[6]];
}
}
close IN;
%t = coord_filter(\%t);
for my $k (sort {$a cmp $b} keys %t){
my @l = @{$t{$k}};
my $pair = "$l[0]-$l[3]";
push @{$h{$pair}}, \@l;
}
return %h;
}
sub load_prior{
my $f = shift @_;
my %h;
open IN,'<',$f;
while(<IN>){
chomp;
my @l =split/\s+/;
$h{"$l[0]-$l[1]"} = 1;
$h{"$l[1]-$l[0]"} = 1;
}
close IN;
return %h;
}