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riboTrap.pl
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riboTrap.pl
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#!/usr/bin/perl
# (c) [email protected]
# part of the riboFrame v1.0 package
$ver = '20191116';
# WARNINNG: THIS SCRIPT ASSUMES THAT SEQUENCES ARE WRITTEN IN JUST 1 LINE AFTER THE HEADER
if (!$ARGV[0]) {
print "\n----------- riboTrap ---------\n------- riboFrame v1.0 -------\n------- rev. $ver --------\n(c) matteo.ramazzotti\@unifi.it\n\n";
print "USAGE: riboTrap.pl sample1 [sample2] [sample3] ... [sampleN] [nopair]\n\n";
exit;
}
@samples = @ARGV;
$nopair = 1 if ($samples[$#samples] eq 'nopair');
pop @samples if ($samples[$#samples] eq 'nopair');
foreach $sam (@samples) {
%r1bf = (); %r1br = (); %r2bf = (); %r2br = (); %rb = (); %flagb = (); %seq = (); %cnta = ();
%r1af = (); %r1ar = (); %r2af = (); %r2ar = (); %ra = (); %flagb = (); %seq = (); %cntb = ();
$base1 = "$sam" if ($nopair);
$base1 = "$sam.1" if (!$nopair);
foreach $beast (qw/bact arch/) {
print STDERR "\nParsing predictions of $beast ribosome on $sam\n";
print STDERR " Loading pair 1 fwd $beast..." if (!$nopair);
print STDERR " Loading fwd $beast..." if ($nopair);
# print STDERR "$sam/$sam.1.fwd.$beast.ribosomal.table\n";
open(IN,"$base1.fwd.$beast.ribosomal.table") or die "no 1.fwd.$beast file";
while($line = <IN>) {
next if ($line =~ /#/);
@tmp = split (/\s+/,$line);
next if ($tmp[18]-$tmp[17] < 60);
$tmp[0] =~ s/\/\d$//; # to cope with pair annotation
$r1bf{$tmp[0]} = 1 if ($beast eq 'bact');
$rb{$tmp[0]} = 1 if ($beast eq 'bact');
$r1af{$tmp[0]} = 1 if ($beast eq 'arch');
$ra{$tmp[0]} = 1 if ($beast eq 'arch');
$r1fposb{$tmp[0]} = $tmp[15].".".$tmp[16] if ($beast eq 'bact');
$r1fposa{$tmp[0]} = $tmp[15].".".$tmp[16] if ($beast eq 'arch');
# print STDERR $tmp[15].".".$tmp[16]," is $tmp[0] = ",$r1fposb{$tmp[0]}," = ",$r1fposa{$tmp[0]} if ($tmp[0] eq 'HWUSI-EAS574_103088163:6:26:6229:19857');
}
close IN;
print STDERR "done.\n Loading pair 1 rev $beast..." if (!$nopair);
print STDERR "done.\n Loading rev $beast..." if ($nopair);
open(IN,"$base1.rev.$beast.ribosomal.table") or die "no 1.rev.$beast file";
while ($line = <IN>) {
next if ($line =~ /#/);
@tmp = split (/\s+/,$line);
next if ($tmp[18]-$tmp[17] < 60);
$tmp[0] =~ s/\/\d$//; # to cope with pair annotation
$r1br{$tmp[0]} = 1 if ($beast eq 'bact');
$rb{$tmp[0]} = 1 if ($beast eq 'bact');
$r1ar{$tmp[0]} = 1 if ($beast eq 'arch');
$ra{$tmp[0]} = 1 if ($beast eq 'arch');
$r1rposb{$tmp[0]} = $tmp[15].".".$tmp[16] if ($beast eq 'bact');
$r1rposa{$tmp[0]} = $tmp[15].".".$tmp[16] if ($beast eq 'arch');
# print STDERR $tmp[15].".".$tmp[16]," is $tmp[0] = ",$r1rposb{$tmp[0]}," = ",$r1rposa{$tmp[0]} if ($tmp[0] eq 'HWUSI-EAS574_103088163:6:26:6229:19857');
}
close IN;
print STDERR "done.\n";
if (!$nopair) {
print STDERR " Loading pair 2 fwd $beast...";
$base2 = "$sam" if ($nopair);
$base2 = "$sam.2" if (!$nopair);
open(IN,"$base2.fwd.$beast.ribosomal.table") or die "no 2.fwd.$beast file";
while($line = <IN>) {
next if ($line =~ /#/);
@tmp = split (/\s+/,$line); # tmp[0] is the read name
next if ($tmp[18]-$tmp[17] < 60);
$tmp[0] =~ s/\/\d$//; # to cope with pair annotation
$r2bf{$tmp[0]} = 1 if ($beast eq 'bact');
$rb{$tmp[0]} = 1 if ($beast eq 'bact');
$r2af{$tmp[0]} = 1 if ($beast eq 'arch');
$ra{$tmp[0]} = 1 if ($beast eq 'arch');
$r2fposb{$tmp[0]} = $tmp[15].".".$tmp[16] if ($beast eq 'bact');
$r2fposa{$tmp[0]} = $tmp[15].".".$tmp[16] if ($beast eq 'arch');
print STDERR $tmp[15].".".$tmp[16]," is $tmp[0] = ",$r2fposb{$tmp[0]}," = ",$r2fposa{$tmp[0]} if ($tmp[0] eq 'HWUSI-EAS574_103088163:6:26:6229:19857');
}
close IN;
print STDERR "done.\n Loading pair 2 rev $beast...";
open(IN,"$base2.rev.$beast.ribosomal.table") or die "no 2.rev.$beast file";
while($line = <IN>) {
next if ($line =~ /#/);
@tmp = split (/\s+/,$line); # tmp[0] is the read name
next if ($tmp[18]-$tmp[17] < 60);
$tmp[0] =~ s/\/\d$//; # to cope with pair annotation
$r2br{$tmp[0]} = 1 if ($beast eq 'bact');
$rb{$tmp[0]} = 1 if ($beast eq 'bact');
$r2ar{$tmp[0]} = 1 if ($beast eq 'arch');
$ra{$tmp[0]} = 1 if ($beast eq 'arch');
$r2rposb{$tmp[0]} = $tmp[15].".".$tmp[16] if ($beast eq 'bact');
$r2rposa{$tmp[0]} = $tmp[15].".".$tmp[16] if ($beast eq 'arch');
print STDERR $tmp[15].".".$tmp[16]," is $tmp[0] = ",$r2rposb{$tmp[0]}," = ",$r2rposa{$tmp[0]} if ($tmp[0] eq 'HWUSI-EAS574_103088163:6:26:6229:19857');
}
close IN;
print STDERR "done.\n";
}
}
# pair1--> <--pair2 == out
# F F trash, it is impossible
# R R trash, it is impossible
# F R 1f2r
# R F 1r2f
# F o 1f
# R o 1r
# o F 2f
# o R 2r
print STDERR "\nFlagging bacterial sequences...";
$err = 0;
foreach $r (keys %rb) { # see the scheme above
$err++ if (($r1bf{$r} && $r2bf{$r}) || ($r1br{$r} && $r2br{$r}));
next if (($r1bf{$r} && $r2bf{$r}) || ($r1br{$r} && $r2br{$r}));
$flagb{$r} = "1f2r" if ($r1bf{$r} && $r2br{$r});
$flagb{$r} = "1r2f" if ($r1br{$r} && $r2bf{$r});
$flagb{$r} = "1f" if ($r1bf{$r} && !$r2br{$r});
$flagb{$r} = "1r" if ($r1br{$r} && !$r2bf{$r});
$flagb{$r} = "2f" if (!$r1br{$r} && $r2bf{$r});
$flagb{$r} = "2r" if (!$r1bf{$r} && $r2br{$r});
# print STDERR "\n$r $flagb{$r} $r2rposb{$r}\n" if ($r eq 'HWUSI-EAS574_103088163:6:26:6229:19857');
$cntb{$flagb{$r}}++;
}
print STDERR "done.\n";
print STDERR " reads: ",scalar keys %rb, "\n";
print STDERR " dir/rev errors $err\n";
print STDERR " flags: ",scalar keys %flagb,"\n";
print STDERR " 1f: $cntb{'1f'}, 1r: $cntb{'1r'}\n";
print STDERR " 2f: $cntb{'2f'}, 2r: $cntb{'2r'}\n";
print STDERR " 1r2f: $cntb{'1r2f'}, 1f2r: $cntb{'1f2r'}\n";
print STDERR "\nFlagging archaeal sequences...";
$err = 0;
foreach $r (keys %ra) { # see the scheme above
$err++ if (($r1af{$r} && $r2af{$r}) || ($r1ar{$r} && $r2ar{$r}));
next if (($r1af{$r} && $r1ar{$r}) || ($r2af{$r} && $r2ar{$r}));
$flaga{$r} = "1f2r" if ($r1af{$r} && $r2ar{$r});
$flaga{$r} = "1r2f" if ($r1ar{$r} && $r2af{$r});
$flaga{$r} = "1f" if ($r1af{$r} && !$r2ar{$r});
$flaga{$r} = "1r" if ($r1ar{$r} && !$r2af{$r});
$flaga{$r} = "2f" if (!$r1ar{$r} && $r2af{$r});
$flaga{$r} = "2r" if (!$r1af{$r} && $r2ar{$r});
$cnta{$flaga{$r}}++;
}
print STDERR "done.\n";
print STDERR " reads: ",scalar keys %ra, "\n";
print STDERR " dir/rev errors $err\n";
print STDERR " flags: ",scalar keys %flaga,"\n";
print STDERR " 1f: $cnta{'1f'}, 1r: $cnta{'1r'}\n";
print STDERR " 2f: $cnta{'2f'}, 2r: $cnta{'2r'}\n";
print STDERR " 1r2f: $cnta{'1r2f'}, 1f2r: $cnta{'1f2r'}\n";
print STDERR "\nLoading pair1 sequences from $base1.fasta\n";
$cnt1a = 0; $cnt1b = 0;
open(IN,"$base1.fasta");
$t = 0;
while(<IN>) {
chomp $_;
if ($_ =~ />/) {
$t++;
$name = $_;
$name =~ s/>//;
$name =~ s/ .+//; # this is because hmmsearch cuts fasta headers at the first space as blast...
$name =~ s/\/1//;
$name =~ s/ +$//;
$ok = 0;
next if (!$flagb{$name} && !$flaga{$name});
# next if (($flagb{$name} && $flaga{$name})); # the same read is attributed to both archea and bacteria, this is not good...
$ok = 1;
next;
}
if ($ok) {
if ($flagb{$name} =~ /1f/) {
# ($st,$en) = split (/\./,$r1fposb{$name});
# $st--;
# $post = 1515-$st-length($_);
$seq1b{$name} = $_;
$len1b{$name} = length($_);
# $seq1bfull{$name} = "-"x$st.$_."-"x$post;# if ($seqb{$name});
$posb{"1f@".$name} = $r1fposb{$name};
$position1b{$name} = $r1fposb{$name};
# print "1f @ $name: ",$posb{"1f@".$name},"\n";
# <STDIN>;
$cnt1b++;
print STDERR "\n",$name.": b1f:".$r1fposb{$name}.":",$position1b{$name},"\n" if ($name eq 'HWUSI-EAS574_103088163:6:26:6229:19857');
}
if ($flagb{$name} =~ /1r/) {
# ($st,$en) = split (/\./,$r1rposb{$name});
# $st--;
# $post = 1515-$st-length($_);
$_ = reverse($_);
$_ =~ tr/ATGC/TACG/;
$seq1b{$name} .= $_;
$len1b{$name} = length($_);
# $seq1bfull{$name} = "-"x$st.$_."-"x$post;# if ($seqb{$name});
$posb{"1r@".$name} = $r1rposb{$name};
$position1b{$name} = $r1rposb{$name};
$cnt1b++;
print STDERR "\n",$name.": b1r:".$r1rposb{$name}.":",$position2b{$name},"\n" if ($name eq 'HWUSI-EAS574_103088163:6:26:6229:19857');
}
if ($flaga{$name} =~ /1f/) {
# ($st,$en) = split (/\./,$r1fposa{$name});
# $st--;
# $post = 1465-$st-length($_);
$seq1a{$name} = $_;
$len1a{$name} = length($_);
# $seq1afull{$name} = "-"x$st.$_."-"x$post;# if ($seqb{$name});
$posa{"1f@".$name} = $r1fposa{$name};
$position1a{$name} = $r1fposa{$name};
$cnt1a++;
print STDERR "\n",$name.": a1f".$r1fposa{$name}.":",$position1a{$name},"\n" if ($name eq 'HWUSI-EAS574_103088163:6:26:6229:19857');
}
if ($flaga{$name} =~ /1r/) {
# ($st,$en) = split (/\./,$r1rposa{$name});
# $st--;
# $post = 1465-$st-length($_);
$_ = reverse($_);
$_ =~ tr/ATGC/TACG/;
$seq1a{$name} = $_;
$len1a{$name} = length($_);
# $seq1afull{$name} = "-"x$st.$_."-"x$post;# if ($seqb{$name});
$posa{"1r@".$name} = $r1rposa{$name};
$position1a{$name} = $r1rposa{$name};
$cnt1a++;
print STDERR "\n",$name.": a1r".$r1rposa{$name}.":",$position1a{$name},"\n" if ($name eq 'HWUSI-EAS574_103088163:6:26:6229:19857');
}
#print STDERR "\r $cnt1b + $cnt1a / $t good sequences\n";
}
}
close IN;
print STDERR "\n done. $cnt1b bacterial and $cnt1a archeal valid reads.\n";
if (!$nopair) {
print STDERR "\nLoading pair2 sequences from $base2.fasta\n";
# open(IN,"/media/SATA1/metagenomics/reads/$sam"."2.fasta");
open(IN,"$base2.fasta");
$cnt2a = 0; $cnt2b = 0;
$t = 0;
while(<IN>) {
chomp $_;
if ($_ =~ />/) {
$t++;
$name = $_;
$name =~ s/>//;
$name =~ s/\/2//;
$name =~ s/ +$//;
$ok = 0;
next if (!$flagb{$name} && !$flaga{$name});
# next if (($flagb{$name} && $flaga{$name})); # the same read is attributed to both archea and bacteria, this is not good...
$ok = 1;
next;
}
if ($ok) {
if ($flagb{$name} =~ /2f/) {
# ($st,$en) = split (/\./,$r2fposb{$name});
# $st--;
# $post = 1515-$st-length($_);
$seq2b{$name} = $_;# if (!$seqb{$name});
$len2b{$name} = length($_);
# $seq2bfull{$name} = "-"x$st.$_."-"x$post;# if ($seqb{$name});
$posb{"2f@".$name} = $r2fposb{$name};
$position2b{$name} = $r2fposb{$name};
print STDERR "\n",$name.": b2f:".$r2fposb{$name}.":",$position2b{$name},"\n" if ($name eq 'HWUSI-EAS574_103088163:6:26:6229:19857');
$cnt2b++;
}
if ($flagb{$name} =~ /2r/) {
# ($st,$en) = split (/\./,$r2rposb{$name});
# $st--;
# $post = 1515-$st-length($_);
$_ = reverse($_);
$_ =~ tr/ATGC/TACG/;
$seq2b{$name} = $_;# if (!$seqb{$name});
$len2b{$name} = length($_);
# $seq2bfull{$name} = "-"x$st.$_."-"x$post;# if ($seqb{$name});
# $seq2b{$name} .= "NNNNNNNNNN".$_ if ($seqb{$name});
$posb{"2r@".$name} = $r2rposb{$name};
$position2b{$name} = $r2rposb{$name};
print STDERR "\n",$name.": b2r:".$r2rposb{$name}.":",$position2b{$name},"\n" if ($name eq 'HWUSI-EAS574_103088163:6:26:6229:19857');
$cnt2b++;
}
if ($flaga{$name} =~ /2f/) {
# ($st,$en) = split (/\./,$r2fposa{$name});
# $st--;
# $post = 1465-$st-length($_);
$seq2a{$name} = $_;# if (!$seqa{$name});
$len2a{$name} = length($_);
# $seq2afull{$name} = "-"x$st.$_."-"x$post;# if ($seqb{$name});
# $seq2a{$name} .= "NNNNNNNNNN".$_ if ($seqa{$name});
$posa{"2f@".$name} = $r2fposa{$name};
$position2a{$name} = $r2fposa{$name};
print STDERR "\n",$name.": a2f:".$r2fposa{$name}.":",$position2b{$name},"\n" if ($name eq 'HWUSI-EAS574_103088163:6:26:6229:19857');
$cnt2a++;
}
if ($flaga{$name} =~ /2r/) {
# ($st,$en) = split (/\./,$r2rposa{$name});
# $st--;
# $post = 1465-$st-length($_);
$_ = reverse($_);
$_ =~ tr/ATGC/TACG/;
$seq2a{$name} = $_;# if (!$seqa{$name});
$len2a{$name} = length($_);
# $seq2afull{$name} = "-"x$st.$_."-"x$post;# if ($seqb{$name});
# $seq2a{$name} .= "NNNNNNNNNN".$_ if ($seqa{$name});
$posa{"2r@".$name} = $r2rposa{$name};
$position2a{$name} = $r2rposa{$name};
print STDERR "\n",$name.": a2r:".$r2rposa{$name}.":",$position2b{$name},"\n" if ($name eq 'HWUSI-EAS574_103088163:6:26:6229:19857');
$cnt2a++;
}
#print STDERR "\r $cnt2b + $cnt2a / $t good sequences";
}
}
close IN;
print STDERR "\n done. $cnt2b bacterial and $cnt2a archeal valid reads.\n";
}
$goodb = $cnt1b + $cnt2b;
$gooda = $cnt1a + $cnt2a;
# $sam = 'tmp';
open(OUTB, ">$sam.bact.16S.fasta");
open(OUTA, ">$sam.arch.16S.fasta");
open(OUTC, ">$sam.16S.fasta");
# open(OUTD, ">$sam.16S.full.fasta");
open(COVB, ">$sam.bact.16S.coverage");
open(COVA, ">$sam.arch.16S.coverage");
open(COVC, ">$sam.16S.coverage");
print STDERR "\nWriting $goodb bacterial sequences to $sam.bact.16S.fasta...";
%used1 = ();
%used2 = ();
foreach $name (keys %seq1b) {
$namea = $name;
$namea .= ":".$len1b{$name}.":".$position1b{$name};
print "\n$name:$namea\n" if (!$position1b{$name});
# <STDIN> if (!$position1b{$name});
print OUTB ">",$namea,"\n",$seq1b{$name},"\n";
print OUTC ">",$namea,"\n",$seq1b{$name},"\n";
# print OUTD ">",$name,"\n",$seq1bfull{$name},"\n";
push (@pos,$position1b{$name});
$used1{$name} = 1;
}
foreach $name (keys %seq2b) {
$namea = $name;
$namea .= ":".$len2b{$name}.":".$position2b{$name};
print "\n$name:$namea\n" if (!$position2b{$name});
<STDIN> if (!$position2b{$name});
print OUTB ">",$namea,"\n",$seq2b{$name},"\n";
print OUTC ">",$namea,"\n",$seq2b{$name},"\n";
# print OUTD ">",$name,"\n",$seq2bfull{$name},"\n";
push (@pos,$position2b{$name});
$used2{$name} = 1;
}
close OUTB;
print STDERR "done.\n";
print STDERR "Writing $gooda archeal sequences to $sam.arch.16S.fasta...";
foreach $name (keys %seq1a) {
$namea = $name;
$namea .= ":".$len1a{$name}.":".$position1a{$name};
print "\n$name:$namea\n" if (!$position1a{$name});
<STDIN> if (!$position1a{$name});
print OUTA ">",$namea,"\n",$seq1a{$name},"\n";
print OUTC ">",$namea,"\n",$seq1a{$name},"\n" if (!$used1{$name});
# print OUTD ">",$name,"\n",$seq1afull{$name},"\n" if (!$used1{$name});
push (@pos,$position1a{$name}) if (!$used1{$name});
$used1{$name} = 1;
}
foreach $name (keys %seq2a) {
$namea = $name;
$namea .= ":".$len2a{$name}.":".$position2a{$name};
print "\n$name:$namea\n" if (!$position2a{$name});
<STDIN> if (!$position2a{$name});
print OUTA ">",$namea,"\n",$seq2a{$name},"\n";
print OUTC ">",$namea,"\n",$seq2a{$name},"\n" if (!$used2{$name});
# print OUTD ">",$name,"\n",$seq2afull{$name},"\n" if (!$used2{$name});
push (@pos,$position2a{$name}) if (!$used2{$name});
$used2{$name} = 1;
}
close OUTB;
close OUTC;
# close OUTD;
$merge = (scalar keys %used1) + (scalar keys %used2);
print STDERR "done.\n\n", scalar keys %used1," pair1 + ", scalar keys %used2, " pair2 = $merge reads also written in merged file $sam.16S.fasta\n\n";
print STDERR " Writing ribosome coverage table to $sam.coverage...";
%cnta = ();
foreach $r (@pos) {
($st,$en) = split (/\./,$r);
for ($pos=$st;$pos<=$en;$pos++) {
$cnta{$pos}++;
}
}
print COVC "pos\tcnt\n";
foreach $pos (1..1515) {
$cnta{$pos} = 0 if (!$cnta{$pos});
print COVC $pos,"\t",$cnta{$pos},"\n";
}
print STDERR "done.\n";
close COVC;
print STDERR " Writing bacterial ribosome coverage table to $sam.bact.coverage...";
# $okb = 1;
%cnt1 = ();
%cnt2 = ();
%cnt = ();
foreach $name (keys %posb) {
# print "$name: ", $posb{"1f@".$name}," - ",$posb{"1r@".$name}," - ", $posb{"2f@".$name}," - ",$posb{"2r@".$name},"\n";
# $w = <STDIN> if (!$okb);
# $okb = 1 if ($w =~ /\w/);
$name =~ s/^...//;
if ($posb{"1f@".$name}) {
($st,$en) = split (/\./,$posb{"1f@".$name});
# print "1f: $st -> $en\n";
for ($pos=$st;$pos<=$en;$pos++) {
$cnt1{$pos}++;
$cnt{$pos}++;
}
}
if ($posb{"1r@".$name}) {
($st,$en) = split (/\./,$posb{"1r@".$name});
# print "1r: $st -> $en\n";
for ($pos=$st;$pos<=$en;$pos++) {
$cnt1{$pos}++;
$cnt{$pos}++;
}
}
if ($posb{"2f@".$name}) {
($st,$en) = split (/\./,$posb{"2f@".$name});
# print "2f: $st -> $en\n";
for ($pos=$st;$pos<=$en;$pos++) {
$cnt2{$pos}++;
$cnt{$pos}++;
}
}
if ($posb{"2r@".$name}) {
($st,$en) = split (/\./,$posb{"2r@".$name});
# print "2r: $st -> $en\n";
for ($pos=$st;$pos<=$en;$pos++) {
$cnt2{$pos}++;
$cnt{$pos}++;
}
}
}
print COVB "pos\tread1\tread2\tboth\n";
foreach $pos (1..1515) {
$cnt1{$pos} = 0 if (!$cnt1{$pos});
$cnt2{$pos} = 0 if (!$cnt2{$pos});
print COVB $pos,"\t",$cnt1{$pos},"\t",$cnt2{$pos},"\t",$cnt{$pos},"\n";
}
print STDERR "done.\n";
close COVB;
print STDERR " Writing archeal ribosome coverage table to $sam.arch.coverage...";
# $oka = 1;
%cnt1 = ();
%cnt2 = ();
%cnt = ();
foreach $name (keys %posa) {
# print "$name: ", $posa{"1f@".$name}," - ",$posa{"1r@".$name}," - ", $posa{"2f@".$name}," - ",$posa{"2r@".$name},"\n";
# $w = <STDIN> if (!$oka);
# $oka = 1 if ($w =~ /\w/);
$name =~ s/^...//;
if ($posa{"1f@".$name}) {
($st,$en) = split (/\./,$posa{"1f@".$name});
# print "1f: $st -> $en\n";
for ($pos=$st;$pos<=$en;$pos++) {
$cnt1{$pos}++;
$cnt{$pos}++;
}
}
if ($posa{"1r@".$name}) {
($st,$en) = split (/\./,$posa{"1r@".$name});
# print "1r: $st -> $en\n";
for ($pos=$st;$pos<=$en;$pos++) {
$cnt1{$pos}++;
$cnt{$pos}++;
}
}
if ($posa{"2f@".$name}) {
($st,$en) = split (/\./,$posa{"2f@".$name});
# print "2f: $st -> $en\n";
for ($pos=$st;$pos<=$en;$pos++) {
$cnt2{$pos}++;
$cnt{$pos}++;
}
}
if ($posa{"2r@".$name}) {
($st,$en) = split (/\./,$posa{"2r@".$name});
# print "2r: $st -> $en\n";
for ($pos=$st;$pos<=$en;$pos++) {
$cnt2{$pos}++;
$cnt{$pos}++;
}
}
}
print COVA "pos\tread1\tread2\tboth\n";
foreach $pos (1..1465) {
$cnt1{$pos} = 0 if (!$cnt1{$pos});
$cnt2{$pos} = 0 if (!$cnt2{$pos});
print COVA $pos,"\t",$cnt1{$pos},"\t",$cnt2{$pos},"\t",$cnt{$pos},"\n";
}
print STDERR "done.\n";
close OUT;
close COVA;
close COVB;
}