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|
#!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use WigParser;
my $usage = "usage: $0 strand_coverage.wig strand[+-]\n\n";
# need strand value to include in the GFF file.
my $wig_file = $ARGV[0] or die $usage;
my $strand = $ARGV[1] or die $usage;
main: {
my $scaffold = "";
my $lend = undef;
my $rend = undef;
open (my $fh, $wig_file) or die "Error, cannot open file $wig_file";
while (<$fh>) {
chomp;
if (/variableStep chrom=(\S+)/) {
if ($lend && $rend) {
print "$scaffold\tpartition\tregion\t$lend\t$rend\t.\t$strand\t.\t.\n";
$lend = undef;
$rend = undef;
}
$scaffold = $1;
next;
}
my @x = split(/\t/);
my ($pos, $cov) = @x;
if ($cov) {
if (! defined $lend) {
$lend = $pos;
$rend = $pos;
}
else {
$rend = $pos;
}
}
else {
# no coverage... may have ended a block.
if ($lend) {
# report coverage block:
my $len = $rend - $lend + 1;
print "$scaffold\tpartition\tregion\t$lend\t$rend\t.\t$strand\t.\t.\t$len\n";
# reinit
$lend = undef;
$rend = undef;
}
}
}
# get last block
if ($lend && $rend) {
print "$scaffold\tpartition\tregion\t$lend\t$rend\t.\t$strand\t.\t.\n";
}
exit(0);
}
|
