94 lines
1.9 KiB
Perl
94 lines
1.9 KiB
Perl
#!/usr/bin/env perl
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use strict;
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use warnings;
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use FindBin;
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use lib ("$FindBin::RealBin/../../PerlLib");
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use SAM_reader;
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use SAM_entry;
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use Overlap_piler;
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my $usage = "usage: $0 file.sam\n\n";
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my $sam_file = $ARGV[0] or die $usage;
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main: {
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my $sam_reader = new SAM_reader($sam_file);
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my %core_to_coords;
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while ($sam_reader->has_next()) {
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my $sam_entry = $sam_reader->get_next();
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if ($sam_entry->is_query_unmapped()) {
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next;
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}
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my $read_name = $sam_entry->get_read_name();
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my $scaff_name = $sam_entry->get_scaffold_name();
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my $strand = $sam_entry->get_query_strand();
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my ($genome_coords_aref, $query_coords_aref) = $sam_entry->get_alignment_coords();
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my $core_scaff = join("$;", $sam_entry->get_core_read_name(), $scaff_name);
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my @coords;
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foreach my $segment (@$genome_coords_aref) {
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my ($lend, $rend) = @$segment;
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push (@{$core_to_coords{$core_scaff}}, [$lend, $rend]);
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}
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}
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foreach my $core_scaff (keys %core_to_coords) {
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my @coords = @{$core_to_coords{$core_scaff}};
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my ($read_core_name, $scaff_name) = split(/$;/, $core_scaff);
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@coords = sort {$a<=>$b} @coords;
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@coords = &Overlap_piler::simple_coordsets_collapser(@coords);
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my $span_lend = $coords[0]->[0];
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my $span_rend = $coords[$#coords]->[1];
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my @lengths;
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my @starts;
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my $num_segments = 0;
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foreach my $segment (@coords) {
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my ($lend, $rend) = @$segment;
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my $length = $rend - $lend + 1;
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push (@lengths, $length);
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push (@starts, $lend - $span_lend);
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$num_segments++;
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}
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$span_lend--; # coordinate is zero-based, and rend is exclusive
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print join("\t",
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$scaff_name,
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$span_lend,
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$span_rend,
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$read_core_name,
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0,
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"+",
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$span_lend,
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$span_rend,
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".",
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$num_segments,
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join(",", @lengths),
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join(",", @starts),
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) . "\n";
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}
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exit(0);
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}
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