Mercurial > repos > ryanmorin > nextgen_variant_identification
view SNV/SNVMix2_source/SNVMix2-v0.12.1-rc1/samtools-0.1.6/misc/samtools.pl @ 0:74f5ea818cea
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author | ryanmorin |
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date | Wed, 12 Oct 2011 19:50:38 -0400 |
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#!/usr/bin/perl -w # Author: lh3 use strict; use warnings; use Getopt::Std; my $version = '0.3.3'; &usage if (@ARGV < 1); my $command = shift(@ARGV); my %func = (showALEN=>\&showALEN, pileup2fq=>\&pileup2fq, varFilter=>\&varFilter, unique=>\&unique, uniqcmp=>\&uniqcmp); die("Unknown command \"$command\".\n") if (!defined($func{$command})); &{$func{$command}}; exit(0); # # showALEN # sub showALEN { die(qq/Usage: samtools.pl showALEN <in.sam>\n/) if (@ARGV == 0 && -t STDIN); while (<>) { my @t = split; next if (/^\@/ || @t < 11); my $l = 0; $_ = $t[5]; s/(\d+)[MI]/$l+=$1/eg; print join("\t", @t[0..5]), "\t$l\t", join("\t", @t[6..$#t]), "\n"; } } # # varFilter # sub varFilter { my %opts = (d=>3, D=>100, l=>30, Q=>25, q=>10, G=>25, s=>100, w=>10, W=>10, N=>2, p=>undef); getopts('pq:d:D:l:Q:w:W:N:G:', \%opts); die(qq/ Usage: samtools.pl varFilter [options] <in.cns-pileup> Options: -Q INT minimum RMS mapping quality for SNPs [$opts{Q}] -q INT minimum RMS mapping quality for gaps [$opts{q}] -d INT minimum read depth [$opts{d}] -D INT maximum read depth [$opts{D}] -G INT min indel score for nearby SNP filtering [$opts{G}] -w INT SNP within INT bp around a gap to be filtered [$opts{w}] -W INT window size for filtering dense SNPs [$opts{W}] -N INT max number of SNPs in a window [$opts{N}] -l INT window size for filtering adjacent gaps [$opts{l}] -p print filtered variants \n/) if (@ARGV == 0 && -t STDIN); # calculate the window size my ($ol, $ow, $oW) = ($opts{l}, $opts{w}, $opts{W}); my $max_dist = $ol > $ow? $ol : $ow; $max_dist = $oW if ($max_dist < $oW); # the core loop my @staging; # (indel_filtering_score, flt_tag) while (<>) { my @t = split; next if (uc($t[2]) eq uc($t[3]) || $t[3] eq '*/*'); # skip non-var sites # clear the out-of-range elements while (@staging) { last if ($staging[0][2] eq $t[0] && $staging[0][3] + $max_dist >= $t[1]); varFilter_aux(shift(@staging), $opts{p}); # calling a function is a bit slower, not much } my ($flt, $score) = (0, -1); # first a simple filter if ($t[7] < $opts{d}) { $flt = 2; } elsif ($t[7] > $opts{D}) { $flt = 3; } # site dependent filters if ($flt == 0) { if ($t[2] eq '*') { # an indel $flt = 1 if ($t[6] < $opts{q}); # filtering SNPs if ($t[5] >= $opts{G}) { for my $x (@staging) { next if ($x->[0] >= 0 || $x->[3] + $ow < $t[1]); $x->[1] = 5 if ($x->[1] == 0); } } # calculate the filtering score (different from indel quality) $score = $t[5]; $score += $opts{s} * $t[10] if ($t[8] ne '*'); $score += $opts{s} * $t[11] if ($t[9] ne '*'); # check the staging list for indel filtering for my $x (@staging) { next if ($x->[0] < 0 || $x->[3] + $ol < $t[1]); if ($x->[0] < $score) { $x->[1] = 6; } else { $flt = 6; last; } } } else { # a SNP $flt = 1 if ($t[6] < $opts{Q}); # check adjacent SNPs my $k = 1; for my $x (@staging) { ++$k if ($x->[0] < 0 && $x->[3] + $oW >= $t[1] && ($x->[1] == 0 || $x->[1] == 4 || $x->[1] == 5)); } # filtering is necessary if ($k > $opts{N}) { $flt = 4; for my $x (@staging) { $x->[1] = 4 if ($x->[0] < 0 && $x->[3] + $oW >= $t[1] && $x->[1] == 0); } } else { # then check gap filter for my $x (@staging) { next if ($x->[0] < 0 || $x->[3] + $ow < $t[1]); if ($x->[0] >= $opts{G}) { $flt = 5; last; } } } } } push(@staging, [$score, $flt, @t]); } # output the last few elements in the staging list while (@staging) { varFilter_aux(shift @staging, $opts{p}); } } sub varFilter_aux { my ($first, $is_print) = @_; if ($first->[1] == 0) { print join("\t", @$first[2 .. @$first-1]), "\n"; } elsif ($is_print) { print STDERR join("\t", substr("UQdDWGgX", $first->[1], 1), @$first[2 .. @$first-1]), "\n"; } } # # pileup2fq # sub pileup2fq { my %opts = (d=>3, D=>255, Q=>25, G=>25, l=>10); getopts('d:D:Q:G:l:', \%opts); die(qq/ Usage: samtools.pl pileup2fq [options] <in.cns-pileup> Options: -d INT minimum depth [$opts{d}] -D INT maximum depth [$opts{D}] -Q INT min RMS mapQ [$opts{Q}] -G INT minimum indel score [$opts{G}] -l INT indel filter winsize [$opts{l}]\n /) if (@ARGV == 0 && -t STDIN); my ($last_chr, $seq, $qual, @gaps, $last_pos); my $_Q = $opts{Q}; my $_d = $opts{d}; my $_D = $opts{D}; $last_chr = ''; while (<>) { my @t = split; if ($last_chr ne $t[0]) { &p2q_post_process($last_chr, \$seq, \$qual, \@gaps, $opts{l}) if ($last_chr); $last_chr = $t[0]; $last_pos = 0; $seq = ''; $qual = ''; @gaps = (); } if ($t[1] - $last_pos != 1) { $seq .= 'n' x ($t[1] - $last_pos - 1); $qual .= '!' x ($t[1] - $last_pos - 1); } if ($t[2] eq '*') { push(@gaps, $t[1]) if ($t[5] >= $opts{G}); } else { $seq .= ($t[6] >= $_Q && $t[7] >= $_d && $t[7] <= $_D)? uc($t[3]) : lc($t[3]); my $q = $t[4] + 33; $q = 126 if ($q > 126); $qual .= chr($q); } $last_pos = $t[1]; } &p2q_post_process($last_chr, \$seq, \$qual, \@gaps, $opts{l}); } sub p2q_post_process { my ($chr, $seq, $qual, $gaps, $l) = @_; &p2q_filter_gaps($seq, $gaps, $l); print "\@$chr\n"; &p2q_print_str($seq); print "+\n"; &p2q_print_str($qual); } sub p2q_filter_gaps { my ($seq, $gaps, $l) = @_; for my $g (@$gaps) { my $x = $g > $l? $g - $l : 0; substr($$seq, $x, $l + $l) = lc(substr($$seq, $x, $l + $l)); } } sub p2q_print_str { my ($s) = @_; my $l = length($$s); for (my $i = 0; $i < $l; $i += 60) { print substr($$s, $i, 60), "\n"; } } # # unique # sub unique { my %opts = (f=>250.0, q=>5, r=>2, a=>1, b=>3); getopts('Qf:q:r:a:b:', \%opts); die("Usage: samtools.pl unique [-f $opts{f}] <in.sam>\n") if (@ARGV == 0 && -t STDIN); my $last = ''; my $recal_Q = !defined($opts{Q}); 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) if (@a); $last = $t[0]; } push(@a, [$score, \@t]); } &unique_aux(\@a, $opts{f}, $recal_Q) if (@a); } sub unique_aux { my ($a, $fac, $is_recal) = @_; my ($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) { 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 = (); } # # uniqcmp: compare two SAM files # sub uniqcmp { my %opts = (q=>10, s=>100); getopts('pq:s:', \%opts); die("Usage: samtools.pl uniqcmp <in1.sam> <in2.sam>\n") if (@ARGV < 2); my ($fh, %a); warn("[uniqcmp] read the first file...\n"); &uniqcmp_aux($ARGV[0], \%a, 0); warn("[uniqcmp] read the second file...\n"); &uniqcmp_aux($ARGV[1], \%a, 1); 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) = @_; 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+)/); $_ = $t[5]; s/(\d+)[MI]/$x+=$1/eg; @{$a->{$t[0]}[$which]} = (($t[1]&0x10)? 1 : 0, $t[2], $t[3]-$l, $t[4], "$x:$nm", $x - 4 * $nm); } close($fh); } # # Usage # sub usage { die(qq/ Program: samtools.pl (helper script for SAMtools) Version: $version Contact: Heng Li <lh3\@sanger.ac.uk>\n Usage: samtools.pl <command> [<arguments>]\n Command: varFilter filtering SNPs and short indels pileup2fq generate fastq from `pileup -c' showALEN print alignment length (ALEN) following CIGAR \n/); }