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|
#!/usr/bin/env perl
use strict;
use warnings;
use lib ("/usr/lib/trinityrnaseq/PerlLib");
use SAM_reader;
use SAM_entry;
my $usage = "usage: $0 blat.nameSorted.sam [num_top_hits=20] [min_per_ID=0]\n\n";
# note min perID is based on read length and blat2sam.pl default scoring with -q 0 -r 0
my $blat_sam = $ARGV[0] or die $usage;
my $num_top_hits = $ARGV[1] || 20;
my $min_per_ID = $ARGV[2] || 0;
main: {
my $sam_reader = new SAM_reader($blat_sam);
while ($sam_reader->has_next()) {
my @entries;
my $sam_entry = $sam_reader->get_next();
push (@entries, $sam_entry);
while ($sam_reader->has_next()
&&
$sam_reader->preview_next()->get_read_name() eq $sam_entry->get_read_name()) {
push (@entries, $sam_reader->get_next());
}
&report_top_hits(@entries);
}
exit(0);
}
####
sub report_top_hits {
my @entries = @_;
@entries = &get_top_hits(@entries);
foreach my $entry (@entries) {
print $entry->toString() . "\n";
}
return;
}
####
sub get_top_hits {
my @entries = @_;
my @structs;
foreach my $entry (@entries) {
my @fields = $entry->get_fields();
my $seq_length = length($entry->get_sequence());
my $min_score = $seq_length - ( ( 1 - ($min_per_ID / 100)) * $seq_length * 3); # perfect_score - (num_mismatches * mismatch_penalty)
my $alignment_field = $fields[11];
$alignment_field =~ /AS:i:(\d+)/ or die "Error, no score reported for " . $entry->toString();
my $score = $1;
unless (defined $score) {
die "Error, no score for " . $entry->toString();
}
#print "MIN_score: $min_score vs. score: $score\n";
if ($score >= $min_score) {
push (@structs, { entry => $entry,
score => $score,
}
);
}
}
@structs = reverse sort {$a->{score}<=>$b->{score}} @structs;
if ($num_top_hits < 0 && scalar(@structs) > 1) {
# multiply mapped reads
# ignoring entry.
return();
}
elsif ($num_top_hits > 0 && scalar (@structs) > $num_top_hits) {
@structs = @structs[0..$num_top_hits-1];
}
## unwrap:
my @ret;
if (@structs) {
my $top_struct = shift @structs;
my $top_score = $top_struct->{score};
push (@ret, $top_struct->{entry});
foreach my $struct (@structs) {
if ($struct->{score} == $top_score) {
push (@ret, $struct->{entry});
}
else {
last;
}
}
}
return(@ret);
}
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