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|
#!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use SAM_reader;
use SAM_entry;
use Carp;
use List::Util qw(min max);
my $usage = "usage: $0 file.sam [debug_flag=0]\n\n";
my $sam_file = $ARGV[0] or die $usage;
my $DEBUG = $ARGV[1];
main: {
my %PATH_COUNTER;
my $sam_reader = new SAM_reader($sam_file);
while ($sam_reader->has_next()) {
my $sam_entry = $sam_reader->get_next();
if ($sam_entry->is_query_unmapped()) {
next;
}
my $read_name = $sam_entry->get_read_name();
if ($read_name =~ /\.p\d$/) {
# not the first path reported.
next;
}
my $sequence = $sam_entry->get_sequence();
if ($sequence eq "*") {
next;
}
my $sam_line = $sam_entry->get_original_line();
if ($DEBUG) {
print "$sam_line\n";
}
my $NM = 0; # full edit distance (includes mismatches and indels)
if ($sam_line =~ /NM:i:(\d+)/) {
$NM = $1;
}
else {
die "Error, couldn't extract num mismatches from sam line: $sam_line";
}
my $cigar_align = $sam_entry->get_cigar_alignment();
my $num_indel_nts = 0;
while($cigar_align =~ /(\d+)[DI]/g) {
$num_indel_nts += $1;
}
my $num_mismatches = $NM - $num_indel_nts;
if ($num_mismatches < 0) {
confess "Error, calculated negative mismatch count from: NM:$NM, indel:$num_indel_nts, cigar: $cigar_align";
}
my $scaff_name = $sam_entry->get_scaffold_name();
my $strand = $sam_entry->get_query_strand();
my ($genome_coords_aref, $query_coords_aref) = $sam_entry->get_alignment_coords();
my $min_coord = 0 + 'inf';
my $max_coord = 0 - 'inf';
my $align_len = 0;
{
foreach my $coordset (@$genome_coords_aref) {
my $seglen = abs($coordset->[1] - $coordset->[0]) + 1;
$align_len += $seglen;
$min_coord = min($min_coord, $coordset->[0], $coordset->[1]);
$max_coord = max($max_coord, $coordset->[0], $coordset->[1]);
if ($DEBUG) {
print STDERR join("\t", $coordset->[0], $coordset->[1], "seglen: $seglen") . "\n";
}
}
}
if ($DEBUG) {
print STDERR "num_mismatches: $num_mismatches, align_length: $align_len\n";
}
my $per_id = sprintf("%.1f", 100 - $num_mismatches/$align_len * 100);
my $align_counter = "$read_name.p" . ++$PATH_COUNTER{$read_name};
my @genome_n_trans_coords;
while (@$genome_coords_aref) {
my $genome_coordset_aref = shift @$genome_coords_aref;
my $trans_coordset_aref = shift @$query_coords_aref;
my ($genome_lend, $genome_rend) = @$genome_coordset_aref;
my ($trans_lend, $trans_rend) = sort {$a<=>$b} @$trans_coordset_aref;
push (@genome_n_trans_coords, [ $genome_lend, $genome_rend, $trans_lend, $trans_rend ] );
}
## merge neighboring features if within a short distance unlikely to represent an intron.
my @merged_coords;
push (@merged_coords, shift @genome_n_trans_coords);
my $MERGE_DIST = 10;
while (@genome_n_trans_coords) {
my $coordset_ref = shift @genome_n_trans_coords;
my $last_coordset_ref = $merged_coords[$#merged_coords];
if ($coordset_ref->[0] - $last_coordset_ref->[1] <= $MERGE_DIST) {
# merge it.
$last_coordset_ref->[1] = $coordset_ref->[1];
if ($strand eq "+") {
$last_coordset_ref->[3] = $coordset_ref->[3];
} else {
$last_coordset_ref->[2] = $coordset_ref->[2];
}
}
else {
# not merging.
push (@merged_coords, $coordset_ref);
}
}
#my $trans_align_len = 0;
#oreach my $coordset_ref (@merged_coords) {
# my ($genome_lend, $genome_rend, $trans_lend, $trans_rend) = @$coordset_ref;
# $trans_align_len += $trans_rend - $trans_lend + 1;
#}
#
#if ($DEBUG) {
# print "interval-based alignment length: $trans_align_len\n";
#
foreach my $coordset_ref (@merged_coords) {
my ($genome_lend, $genome_rend, $trans_lend, $trans_rend) = @$coordset_ref;
print join("\t",
$scaff_name,
"minimap2",
"cDNA_match",
$genome_lend, $genome_rend,
$per_id,
$strand,
".",
"ID=$align_counter;Parent=$align_counter.mrna;Target=$read_name $trans_lend $trans_rend") . "\n";
}
print "\n";
}
exit(0);
}
|
