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#!/usr/bin/env perl
use strict;
my $SEE = 0;
###############
# blat format: # Q=cDNA T=genomic
################
# 0: match
# 1: mis-match
# 2: rep. match
# 3: N's
# 4: Q gap count
# 5: Q gap bases
# 6: T gap count
# 7: T gap bases
# 8: strand
# 9: Q name
# 10: Q size
# 11: Q start
# 12: Q end
# 13: T name
# 14: T size
# 15: T start
# 16: T end
# 17: block count
# 18: block Sizes
# 19: Q starts
# 20: T starts
# 21: Q seqs (pslx format)
# 22: T seqs (pslx format)
#############################################################
## This script filters blat output and extracts only ##
## the top scoring alignment chain for each accession. ##
#############################################################
my $line_num = 0;
my %data;
my $filename = $ARGV[0] or die "\n\nusage: $0 outputfile.psl [num_top_hits=1]\n\n";
my $num_top_hits = $ARGV[1] || 1;
## First Pass, assign scores to entries associated with accessions.
my $scores_file = "$filename.scores";
{
open (my $ofh, ">$scores_file") or "Error, cannot write to file $scores_file";
open (FILE, "$filename");
my $line_num = 0;
while (<FILE>) {
$line_num++;
my @x = split (/\t/);
unless ($x[0] =~ /^\d/) {next;}
my ($matches, $mismatches, $q_gap_num, $t_gap_num, $q_insert, $t_insert) = ($x[0], $x[1], $x[4], $x[6], $x[5], abs($x[7]));
my $score = &calculate_score($matches, $mismatches, $q_gap_num, $t_gap_num, $q_insert, $t_insert);
$score = sprintf("%.2f", $score);
my $accession = $x[9];
print $ofh join("\t", $accession, $score, $line_num) . "\n";
#if ($line_num > 10000) { last; }
}
close FILE;
close $ofh;
}
my $sort_by_score_file = "$scores_file.sort_by_score";
{
## sort the file by accession, score desc
my $cmd = "sort -k1,1 -k2,2nr $scores_file > $sort_by_score_file";
&process_cmd($cmd);
}
my $top_line_file = "$sort_by_score_file.top";
{
open (my $ofh, ">$top_line_file") or die "Error, cannot write to $top_line_file";
## Identify each highest scoring match
my $prev_acc = "";
my $count_reported = 0;
open (my $fh, $sort_by_score_file) or die $!;
while (<$fh>) {
my $line = $_;
chomp;
my ($acc, $score, $line_no) = split(/\t/);
if ($acc ne $prev_acc) {
## highest score comes first.
$prev_acc = $acc;
$count_reported = 0;
}
if ($count_reported < $num_top_hits) {
print $ofh $line;
}
$count_reported++;
}
close $fh;
close $ofh;
}
my $sort_by_line_no_file = "$top_line_file.sort_by_line_no";
{
## now sort by line number
my $cmd = "sort -k3,3n $top_line_file > $sort_by_line_no_file";
&process_cmd($cmd);
}
open (my $lines_fh, $sort_by_line_no_file) or die $!;
my $line = <$lines_fh>;
chomp $line;
my ($acc, $score, $line_no) = split(/\t/, $line);
open (FILE, "$filename");
$line_num = 0;
while (<FILE>) {
my $outline = $_;
$line_num++;
if ($line_num == $line_no) {
print $outline;
## set next search line no
my $line = <$lines_fh>;
if (! $line) {
# no more to search
last;
}
($acc, $score, $line_no) = split(/\t/, $line);
}
elsif ($line_num >$line_no) {
die "Error, $line_num exceeded $line_no";
}
}
close FILE;
## cleanup
unlink($scores_file, $sort_by_score_file, $top_line_file, $sort_by_line_no_file);
exit(0);
####
sub calculate_score {
my ($match, $mismatch, $q_gap_num, $t_gap_num, $q_insert, $t_insert) = @_;
## JKent's code in pslFilter:
# score = (psl->match + psl->repMatch)*reward - psl->misMatch*cost
# - (psl->qNumInsert + psl->tNumInsert + 1) * gapOpenCost
# - log(psl->qBaseInsert + psl->tBaseInsert + 1) * gapSizeLogMod;
#use jkent's default score parameters:
my $reward = 1;
my $cost = 1;
my $gapOpenCost = 4;
my $gapSizeLogMod = 1;
return ( ($match * $reward) - ($mismatch * $cost) -
( ($q_gap_num + $t_gap_num) * $gapOpenCost) -
( log ($q_insert + $t_insert + 1) * $gapSizeLogMod) );
}
####
sub process_cmd {
my ($cmd) = @_;
print STDERR "CMD: $cmd\n";
my $ret = system($cmd);
if ($ret) {
die "Error, cmd: $cmd died with ret $ret";
}
return;
}
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