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|
#!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 partitions.gff clip_pts.wig\n\n";
my $partitions_gff = $ARGV[0] or die $usage;
my $clip_pts_wig = $ARGV[1] or die $usage;
my $MIN_PARTITION_SIZE = 50;
main: {
my %scaff_to_gff = &parse_gff_entries($partitions_gff);
my %scaff_to_clip = &parse_wig_entries($clip_pts_wig);
foreach my $scaff (sort keys %scaff_to_gff) {
my @gffs = @{$scaff_to_gff{$scaff}};
@gffs = sort {$a->{lend}<=>$b->{lend}} @gffs;
my @clips;
if (exists $scaff_to_clip{$scaff}) {
@clips = @{$scaff_to_clip{$scaff}};
@clips = sort {$a<=>$b} @clips;
}
foreach my $gff (@gffs) {
my ($lend, $rend) = ($gff->{lend}, $gff->{rend});
my @overlapping_clips;
if (@clips) {
while (@clips && $clips[0] < $rend) {
my $clip = shift @clips;
if ($clip > $lend) {
push (@overlapping_clips, $clip);
}
}
}
if (@overlapping_clips) {
my @x = @{$gff->{line}};
my $gff_line = join("\t", @x);
#print "$gff_line\nHas overlapping clips: @overlapping_clips\n";
my $prev_lend = $lend;
foreach my $overlapping_clip (@overlapping_clips) {
my $rend = $overlapping_clip - 1;
my @y = @x;
$y[3] = $prev_lend;
$y[4] = $rend;
my $part_length = $rend - $prev_lend + 1;
if ($part_length >= $MIN_PARTITION_SIZE) {
print join("\t", @y) . "\n";
}
$prev_lend = $rend + 1;
#print "$gff_line\nWith clips: " . join("\t", @overlapping_clips) . "\n\n";
}
## report last partition of clip:
$x[3] = $prev_lend;
print join("\t", @x) . "\n";
#print "\n\n";
}
else {
## no clipping. Report original partition.
print join("\t", @{$gff->{line}}) . "\n";
}
}
}
exit(0);
}
####
sub parse_gff_entries {
my ($gff_file) = @_;
my %scaffold_to_gff;
open (my $fh, $gff_file) or die "Error, cannot open file $gff_file";
while (<$fh>) {
chomp;
my @x = split(/\t/);
my $scaff = $x[0];
my $lend = $x[3];
my $rend = $x[4];
my $struct = { line => [@x],
scaff => $scaff,
lend => $lend,
rend => $rend,
};
push (@{$scaffold_to_gff{$scaff}}, $struct);
}
close $fh;
return(%scaffold_to_gff);
}
####
sub parse_wig_entries {
my ($jaccard_file) = @_;
my %scaffold_to_entries;
my $curr_scaff;
open (my $fh, $jaccard_file) or die "Error, cannot open file $jaccard_file";
while (<$fh>) {
unless (/\w/) { next; }
chomp;
if (/^variableStep chrom=(\S+)/) {
$curr_scaff = $1;
next;
}
my ($coord, $val) = split(/\t/);
unless (defined($coord) && defined($val)) {
#die "Error, line $_ lacks expected format";
next;
}
push (@{$scaffold_to_entries{$curr_scaff}}, $coord);
}
close $fh;
return(%scaffold_to_entries);
}
|
