samtools 1.3.1-3 / usr / bin / wgsim_eval.pl

#!/usr/bin/env perl
#
#    Copyright (C) 2009 Genome Research Ltd.
#    Portions copyright (C) 2009-2011 Broad Institute.
#
#    Author: Heng Li <lh3@sanger.ac.uk>
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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# DEALINGS IN THE SOFTWARE.

use strict;
use warnings;
use Getopt::Std;

die (qq/
Usage:   wgsim_eval.pl <command> <arguments>

Command: alneval       evaluate alignment in the SAM format
         vareval       evaluate variant calls in the pileup format
         unique        keep the top scoring hit in SAM
         uniqcmp       compare two alignments without multiple hits
\n/) if (@ARGV == 0);
my $command = shift(@ARGV);
if ($command eq 'alneval') {
    &alneval;
} elsif ($command eq 'vareval') {
    &vareval;
} elsif ($command eq 'unique') {
    &unique;
} elsif ($command eq 'uniqcmp') {
    &uniqcmp;
} else {
    die("[wgsim_eval] unrecognized command.\n");
}
exit;

sub alneval {
    my %opts = (g=>5);
    getopts('pcag:', \%opts);
    die(qq/
Usage:   wgsim_eval.pl alneval [options] <in.sam>\n
Options: -p        print wrong alignments
         -g INT    correct if withint INT of the true coordinate
         -a        generate ROC curves

The default output has columns of mapping quality, number of correct
alignments \/ total number of alignments at that mapping quality,
cumulative sum of number of alignments, and the ratio of cumulative
correct alignments over cumulative total alignments.

The -a option outputs columns with mapping quality, number of mapped
reads with mqual >= the mqual in the first column, and the number of
mismapped reads.  Together they can be used to produce ROC curves for
accuracy of aligners.
\n/) if (@ARGV == 0 && -t STDIN);
    my (@c0, @c1, %fnfp);
    my ($max_q, $flag) = (0, 0);
    my $gap = $opts{g};
    $flag |= 1 if (defined $opts{p});
    $flag |= 2 if (defined $opts{c});
    while (<>) {
        next if (/^\@/);
        my @t = split("\t");
        next if (@t < 11);
        my $line = $_;
        my ($q, $is_correct, $chr, $left, $rght) = (int($t[4]/10), 1, $t[2], $t[3], $t[3]);
        $max_q = $q if ($q > $max_q);
        # right coordinate
        $_ = $t[5]; s/(\d+)[MDN=X]/$rght+=$1,'x'/eg;
        --$rght;
        # correct for clipping
        my ($left0, $rght0) = ($left, $rght);
        $left -= $1 if (/^(\d+)[SH]/);
        $rght += $1 if (/(\d+)[SH]$/);
        $left0 -= $1 if (/(\d+)[SH]$/);
        $rght0 += $1 if (/^(\d+)[SH]/);
        # skip unmapped reads
        next if (($t[1]&0x4) || $chr eq '*');
        # parse read name and check
        if ($t[0] =~ /^(\S+)_(\d+)_(\d+)_/) {
            if ($1 ne $chr) { # different chr
                $is_correct = 0;
            } else {
                if ($flag & 2) {
                    if (($t[1]&0x40) && !($t[1]&0x10)) { # F3, forward
                        $is_correct = 0 if (abs($2 - $left) > $gap && abs($2 - $left0) > $gap);
                    } elsif (($t[1]&0x40) && ($t[1]&0x10)) { # F3, reverse
                        $is_correct = 0 if (abs($3 - $rght) > $gap && abs($3 - $rght0) > $gap);
                    } elsif (($t[1]&0x80) && !($t[1]&0x10)) { # R3, forward
                        $is_correct = 0 if (abs($3 - $left) > $gap && abs($3 - $left0) > $gap);
                    } else { # R3, reverse
                        $is_correct = 0 if (abs($2 - $rght) > $gap && abs($3 - $rght0) > $gap);
                    }
                } else {
                    if ($t[1] & 0x10) { # reverse
                        $is_correct = 0 if (abs($3 - $rght) > $gap && abs($3 - $rght0) > $gap); # in case of indels that are close to the end of a reads
                    } else {
                        $is_correct = 0 if (abs($2 - $left) > $gap && abs($2 - $left0) > $gap);
                    }
                }
            }
        } else {
            warn("[wgsim_eval] read '$t[0]' was not generated by wgsim?\n");
            next;
        }
        ++$c0[$q];
        ++$c1[$q] unless ($is_correct);
        @{$fnfp{$t[4]}} = (0, 0) unless (defined $fnfp{$t[4]});
        ++$fnfp{$t[4]}[0];
        ++$fnfp{$t[4]}[1] unless ($is_correct);
        print STDERR $line if (($flag&1) && !$is_correct && $q > 0);
    }
    # print
    my ($cc0, $cc1) = (0, 0);
    if (!defined($opts{a})) {
        for (my $i = $max_q; $i >= 0; --$i) {
            $c0[$i] = 0 unless (defined $c0[$i]);
            $c1[$i] = 0 unless (defined $c1[$i]);
            $cc0 += $c0[$i]; $cc1 += $c1[$i];
            printf("%.2dx %12d / %-12d  %12d  %.3e\n", $i, $c1[$i], $c0[$i], $cc0, $cc1/$cc0) if ($cc0);
        }
    } else {
        for (reverse(sort {$a<=>$b} (keys %fnfp))) {
            next if ($_ == 0);
            $cc0 += $fnfp{$_}[0];
            $cc1 += $fnfp{$_}[1];
            print join("\t", $_, $cc0, $cc1), "\n";
        }
    }
}

sub vareval {
    my %opts = (g=>10, Q=>200);
    getopts('g:p', \%opts);
    my $skip = $opts{g};
    die("Usage: wgsim_eval.pl vareval [-g $opts{g}] <wgsim.snp> <pileup.flt>\n") if (@ARGV < 1);

    my $is_print = defined($opts{p})? 1 : 0;

    my ($fh, %snp, %indel);
    # read simulated variants
    open($fh, $ARGV[0]) || die;
    while (<$fh>) {
        my @t = split;
        if (@t != 5 || $t[2] eq '-' || $t[3] eq '-') {
            $indel{$t[0]}{$t[1]} = 1;
        } else {
            $snp{$t[0]}{$t[1]} = $t[3];
        }
    }
    close($fh);

    shift(@ARGV);
    my (@cnt);
    for my $i (0 .. 3) {
        for my $j (0 .. $opts{Q}) {
            $cnt[$i][$j] = 0;
        }
    }
    while (<>) {
        my @t = split;
        my $q = $t[5];
        next if ($t[2] eq $t[3]);
        $q = $opts{Q} if ($q > $opts{Q});
        if ($t[2] eq '*') {
            my $hit = 0;
            ++$cnt[2][$q];
            for my $i ($t[1] - $skip .. $t[1] + $skip) {
                if (defined $indel{$t[0]}{$i}) {
                    $hit = 1; last;
                }
            }
            ++$cnt[3][$q] if ($hit == 0);
            print STDERR $_ if ($hit == 0 && $is_print);
        } else {
            ++$cnt[0][$q];
            ++$cnt[1][$q] unless (defined $snp{$t[0]}{$t[1]});
            print STDERR $_ if (!defined($snp{$t[0]}{$t[1]}) && $is_print);
        }
    }

    for (my $i = $opts{Q} - 1; $i >= 0; --$i) {
        $cnt[$_][$i] += $cnt[$_][$i+1] for (0 .. 3);
    }

    for (my $i = $opts{Q}; $i >= 0; --$i) {
        print join("\t", $i, $cnt[0][$i], $cnt[1][$i], $cnt[2][$i], $cnt[3][$i]), "\n";
    }
}

sub unique {
    # -f: parameter to recalute mapping quality
    # -Q: do not recalculate mapping quality
    # -a, -b, -q, -r: scoring system
    my %opts = (f=>250.0, q=>5, r=>2, a=>1, b=>3);
    getopts('Qf:q:r:a:b:m', \%opts);
    die(qq/
Usage:   wgsim_eval.pl unique [options] <in.sam>\n
Options: -Q         recompuate mapping quality from multiple hits
         -f FLOAT   mapQ=FLOAT*(best1-best2)\/best1 [opts{f}]
         -a INT     matching score (when AS tag is absent) [$opts{a}]
         -q INT     gap open penalty [$opts{q}]
         -r INT     gap extension penalty [$opts{r}]
\n/) if (@ARGV == 0 && -t STDIN);
    my $last = '';
    my $recal_Q = defined($opts{Q});
    my $multi_only = defined($opts{m});
    my @a;
    while (<>) {
        my $score = -1;
        print $_ if (/^\@/);
        $score = $1 if (/AS:i:(\d+)/);
        my @t = split("\t");
        next if (@t < 11);
        if ($score < 0) { # AS tag is unavailable
            my $cigar = $t[5];
            my ($mm, $go, $ge) = (0, 0, 0);
            $cigar =~ s/(\d+)[ID]/++$go,$ge+=$1/eg;
            $cigar = $t[5];
            $cigar =~ s/(\d+)M/$mm+=$1/eg;
            $score = $mm * $opts{a} - $go * $opts{q} - $ge * $opts{r}; # no mismatches...
        }
        $score = 1 if ($score < 1);
        if ($t[0] ne $last) {
            &unique_aux(\@a, $opts{f}, $recal_Q, $multi_only) if (@a);
            $last = $t[0];
        }
        push(@a, [$score, \@t]);
    }
    &unique_aux(\@a, $opts{f}, $recal_Q, $multi_only) if (@a);
}

sub unique_aux {
    my ($a, $fac, $is_recal, $multi_only) = @_;
    my ($max, $max2, $max_i) = (0, 0, -1);
    for (my $i = 0; $i < @$a; ++$i) {
        if ($a->[$i][0] > $max) {
            $max2 = $max; $max = $a->[$i][0]; $max_i = $i;
        } elsif ($a->[$i][0] > $max2) {
            $max2 = $a->[$i][0];
        }
    }
    if ($is_recal) {
        if (!$multi_only || @$a > 1) {
            my $q = int($fac * ($max - $max2) / $max + .499);
            $q = 250 if ($q > 250);
            $a->[$max_i][1][4] = $q < 250? $q : 250;
        }
    }
    print join("\t", @{$a->[$max_i][1]});
    @$a = ();
}

sub uniqcmp {
    my %opts = (q=>20, s=>100, b=>4);
    getopts('pq:s:b:', \%opts);
    die(qq/
Usage:   wgsim_eval.pl uniqcmp [options] <in1.sam> <in2.sam>\n
Options: -q INT     confident mapping if mapping quality above INT [$opts{q}]
         -s INT     same mapping if the distance below INT [$opts{s}]
         -b INT     penalty for a difference [$opts{b}]
\n/) if (@ARGV < 2);
    my ($fh, %a);
    warn("[uniqcmp] read the first file...\n");
    &uniqcmp_aux($ARGV[0], \%a, 0, $opts{b});
    warn("[uniqcmp] read the second file...\n");
    &uniqcmp_aux($ARGV[1], \%a, 1, $opts{b});
    warn("[uniqcmp] stats...\n");
    my @cnt;
    $cnt[$_] = 0 for (0..9);
    for my $x (keys %a) {
        my $p = $a{$x};
        my $z;
        if (defined($p->[0]) && defined($p->[1])) {
            $z = ($p->[0][0] == $p->[1][0] && $p->[0][1] eq $p->[1][1] && abs($p->[0][2] - $p->[1][2]) < $opts{s})? 0 : 1;
            if ($p->[0][3] >= $opts{q} && $p->[1][3] >= $opts{q}) {
                ++$cnt[$z*3+0];
            } elsif ($p->[0][3] >= $opts{q}) {
                ++$cnt[$z*3+1];
            } elsif ($p->[1][3] >= $opts{q}) {
                ++$cnt[$z*3+2];
            }
            print STDERR "$x\t$p->[0][1]:$p->[0][2]\t$p->[0][3]\t$p->[0][4]\t$p->[1][1]:$p->[1][2]\t$p->[1][3]\t$p->[1][4]\t",
            $p->[0][5]-$p->[1][5], "\n" if ($z && defined($opts{p}) && ($p->[0][3] >= $opts{q} || $p->[1][3] >= $opts{q}));
        } elsif (defined($p->[0])) {
            ++$cnt[$p->[0][3]>=$opts{q}? 6 : 7];
            print STDERR "$x\t$p->[0][1]:$p->[0][2]\t$p->[0][3]\t$p->[0][4]\t*\t0\t*\t",
            $p->[0][5], "\n" if (defined($opts{p}) && $p->[0][3] >= $opts{q});
        } else {
            print STDERR "$x\t*\t0\t*\t$p->[1][1]:$p->[1][2]\t$p->[1][3]\t$p->[1][4]\t",
            -$p->[1][5], "\n" if (defined($opts{p}) && $p->[1][3] >= $opts{q});
            ++$cnt[$p->[1][3]>=$opts{q}? 8 : 9];
        }
    }
    print "Consistent (high, high):   $cnt[0]\n";
    print "Consistent (high, low ):   $cnt[1]\n";
    print "Consistent (low , high):   $cnt[2]\n";
    print "Inconsistent (high, high): $cnt[3]\n";
    print "Inconsistent (high, low ): $cnt[4]\n";
    print "Inconsistent (low , high): $cnt[5]\n";
    print "Second missing (high):     $cnt[6]\n";
    print "Second missing (low ):     $cnt[7]\n";
    print "First  missing (high):     $cnt[8]\n";
    print "First  missing (low ):     $cnt[9]\n";
}

sub uniqcmp_aux {
    my ($fn, $a, $which, $b) = @_;
    my $fh;
    $fn = "samtools view $fn |" if ($fn =~ /\.bam/);
    open($fh, $fn) || die;
    while (<$fh>) {
        my @t = split;
        next if (@t < 11);
#       my $l = ($t[5] =~ /^(\d+)S/)? $1 : 0;
        my $l = 0;
        my ($x, $nm) = (0, 0);
        $nm = $1 if (/NM:i:(\d+)/);
        $_ = $t[5];
        s/(\d+)[M=XI]/$x+=$1/eg;
        @{$a->{$t[0]}[$which]} = (($t[1]&0x10)? 1 : 0, $t[2], $t[3]-$l, $t[4], "$x:$nm", $x - $b * $nm);
    }
    close($fh);
}