X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=misc%2Fsamtools.pl;h=d03c1c7f148dcca835946e7ccd9ee52f3b6dc00b;hp=c014c52bcf0880d39ba23f567a31396017220142;hb=HEAD;hpb=b27e00385f41769d03a8cca4dbd71275fc9fa906 diff --git a/misc/samtools.pl b/misc/samtools.pl index c014c52..d03c1c7 100755 --- a/misc/samtools.pl +++ b/misc/samtools.pl @@ -6,11 +6,12 @@ use strict; use warnings; use Getopt::Std; -my $version = '0.3.2 (r321)'; +my $version = '0.3.3'; &usage if (@ARGV < 1); my $command = shift(@ARGV); -my %func = (showALEN=>\&showALEN, pileup2fq=>\&pileup2fq, varFilter=>\&varFilter); +my %func = (showALEN=>\&showALEN, pileup2fq=>\&pileup2fq, varFilter=>\&varFilter, plp2vcf=>\&plp2vcf, + unique=>\&unique, uniqcmp=>\&uniqcmp, sra2hdr=>\&sra2hdr, sam2fq=>\&sam2fq); die("Unknown command \"$command\".\n") if (!defined($func{$command})); &{$func{$command}}; @@ -24,9 +25,10 @@ sub showALEN { die(qq/Usage: samtools.pl showALEN \n/) if (@ARGV == 0 && -t STDIN); while (<>) { my @t = split; + next if (/^\@/ || @t < 11); my $l = 0; $_ = $t[5]; - s/(\d+)[SMI]/$l+=$1/eg; + s/(\d+)[MI]/$l+=$1/eg; print join("\t", @t[0..5]), "\t$l\t", join("\t", @t[6..$#t]), "\n"; } } @@ -35,9 +37,21 @@ sub showALEN { # varFilter # +# +# Filtration code: +# +# d low depth +# D high depth +# W too many SNPs in a window (SNP only) +# G close to a high-quality indel (SNP only) +# Q low RMS mapping quality (SNP only) +# g close to another indel with higher quality (indel only) +# s low SNP quality (SNP only) +# i low indel quality (indel only) + sub varFilter { - my %opts = (d=>3, D=>100, l=>30, Q=>25, q=>10, G=>25, s=>100, w=>10, W=>10, N=>2, p=>undef); - getopts('pd:D:l:Q:w:W:N:G:', \%opts); + my %opts = (d=>3, D=>100, l=>30, Q=>25, q=>10, G=>25, s=>100, w=>10, W=>10, N=>2, p=>undef, S=>'', i=>''); + getopts('pq:d:D:l:Q:w:W:N:G:S:i:', \%opts); die(qq/ Usage: samtools.pl varFilter [options] @@ -45,6 +59,8 @@ Options: -Q INT minimum RMS mapping quality for SNPs [$opts{Q}] -q INT minimum RMS mapping quality for gaps [$opts{q}] -d INT minimum read depth [$opts{d}] -D INT maximum read depth [$opts{D}] + -S INT minimum SNP quality [$opts{S}] + -i INT minimum indel quality [$opts{i}] -G INT min indel score for nearby SNP filtering [$opts{G}] -w INT SNP within INT bp around a gap to be filtered [$opts{w}] @@ -65,10 +81,11 @@ Options: -Q INT minimum RMS mapping quality for SNPs [$opts{Q}] my @staging; # (indel_filtering_score, flt_tag) while (<>) { my @t = split; - next if ($t[2] eq $t[3] || $t[3] eq '*/*'); # skip non-var sites + next if (uc($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 >= $t[1]); + # Still on the same chromosome and the first element's window still affects this position? + last if ($staging[0][3] eq $t[0] && $staging[0][4] + $staging[0][2] + $max_dist >= $t[1]); varFilter_aux(shift(@staging), $opts{p}); # calling a function is a bit slower, not much } my ($flt, $score) = (0, -1); @@ -78,14 +95,31 @@ Options: -Q INT minimum RMS mapping quality for SNPs [$opts{Q}] } elsif ($t[7] > $opts{D}) { $flt = 3; } + if ($t[2] eq '*') { # an indel + if ($opts{i} && $opts{i}>$t[5]) { $flt = 8; } + } + elsif ($opts{S} && $opts{S}>$t[5]) { $flt = 7; } # SNP + # site dependent filters + my $len=0; if ($flt == 0) { if ($t[2] eq '*') { # an indel + # If deletion, remember the length of the deletion + my ($a,$b) = split(m{/},$t[3]); + my $alen = length($a) - 1; + my $blen = length($b) - 1; + if ( $alen>$blen ) + { + if ( substr($a,0,1) eq '-' ) { $len=$alen; } + } + elsif ( substr($b,0,1) eq '-' ) { $len=$blen; } + $flt = 1 if ($t[6] < $opts{q}); # filtering SNPs if ($t[5] >= $opts{G}) { for my $x (@staging) { - next if ($x->[0] >= 0 || $x->[3] + $ow < $t[1]); + # Is it a SNP and is it outside the SNP filter window? + next if ($x->[0] >= 0 || $x->[4] + $x->[2] + $ow < $t[1]); $x->[1] = 5 if ($x->[1] == 0); } } @@ -95,7 +129,8 @@ Options: -Q INT minimum RMS mapping quality for SNPs [$opts{Q}] $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 < $t[1]); + # Is it a SNP and is it outside the gap filter window + next if ($x->[0] < 0 || $x->[4] + $x->[2] + $ol < $t[1]); if ($x->[0] < $score) { $x->[1] = 6; } else { @@ -107,17 +142,17 @@ Options: -Q INT minimum RMS mapping quality for SNPs [$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 || $x->[1] == 5)); + ++$k if ($x->[0] < 0 && $x->[4] + $x->[2] + $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); + $x->[1] = 4 if ($x->[0] < 0 && $x->[4] + $x->[2] + $oW >= $t[1] && $x->[1] == 0); } } else { # then check gap filter for my $x (@staging) { - next if ($x->[0] < 0 || $x->[3] + $ow < $t[1]); + next if ($x->[0] < 0 || $x->[4] + $x->[2] + $ow < $t[1]); if ($x->[0] >= $opts{G}) { $flt = 5; last; } @@ -125,7 +160,7 @@ Options: -Q INT minimum RMS mapping quality for SNPs [$opts{Q}] } } } - push(@staging, [$score, $flt, @t]); + push(@staging, [$score, $flt, $len, @t]); } # output the last few elements in the staging list while (@staging) { @@ -136,9 +171,9 @@ Options: -Q INT minimum RMS mapping quality for SNPs [$opts{Q}] sub varFilter_aux { my ($first, $is_print) = @_; if ($first->[1] == 0) { - print join("\t", @$first[2 .. @$first-1]), "\n"; + print join("\t", @$first[3 .. @$first-1]), "\n"; } elsif ($is_print) { - print STDERR join("\t", substr("UQdDWGgX", $first->[1], 1), @$first[2 .. @$first-1]), "\n"; + print STDERR join("\t", substr("UQdDWGgsiX", $first->[1], 1), @$first[3 .. @$first-1]), "\n"; } } @@ -215,25 +250,263 @@ sub p2q_print_str { } # -# varStats +# sam2fq +# + +sub sam2fq { + my %opts = (n=>20, p=>''); + getopts('n:p:', \%opts); + die("Usage: samtools.pl sam2fq [-n 20] [-p ] \n") if (@ARGV == 0 && -t STDIN); + if ($opts{p} && $opts{n} > 1) { + my $pre = $opts{p}; + my @fh; + for (0 .. $opts{n}-1) { + open($fh[$_], sprintf("| gzip > $pre.%.3d.fq.gz", $_)) || die; + } + my $i = 0; + while (<>) { + next if (/^@/); + chomp; + my @t = split("\t"); + next if ($t[9] eq '*'); + my ($name, $seq, $qual); + if ($t[1] & 16) { # reverse strand + $seq = reverse($t[9]); + $qual = reverse($t[10]); + $seq =~ tr/ACGTacgt/TGCAtgca/; + } else { + ($seq, $qual) = @t[9,10]; + } + $name = $t[0]; + $name .= "/1" if ($t[1] & 0x40); + $name .= "/2" if ($t[1] & 0x80); + print {$fh[$i]} "\@$name\n$seq\n"; + if ($qual ne '*') { + print {$fh[$i]} "+\n$qual\n"; + } + $i = 0 if (++$i == $opts{n}); + } + close($fh[$_]) for (0 .. $opts{n}-1); + } else { + die("To be implemented.\n"); + } +} + +# +# sra2hdr # -sub varStats { - my %opts = (d=>'', c=>5); - getopts('d:c:', \%opts); - die("Usage: samtools.pl varStats [-d dbSNP.snp] [-c $opts{c}] \n") if (@ARGV == 0 && -t STDIN); - my (@cnt, %hash); - my $col = $opts{c} - 1; +# This subroutine does not use an XML parser. It requires that the SRA +# XML files are properly formated. +sub sra2hdr { + my %opts = (); + getopts('', \%opts); + die("Usage: samtools.pl sra2hdr \n") if (@ARGV == 0); + my $pre = $ARGV[0]; + my $fh; + # read sample + my $sample = 'UNKNOWN'; + open($fh, "$pre.sample.xml") || die; + while (<$fh>) { + $sample = $1 if (/) { + if (/\s*(\S+)\s*<\/LIBRARY_NAME>/i) { + $exp2lib{$exp} = $1; + } + } + close($fh); + # read run + my ($run, @fn); + open($fh, "$pre.run.xml") || die; + while (<$fh>) { + if (//i) { + if (@fn == 1) { + print STDERR "$fn[0]\t$run\n"; + } else { + for (0 .. $#fn) { + print STDERR "$fn[$_]\t$run", "_", $_+1, "\n"; + } + } + } + } + close($fh); +} + +# +# unique +# + +sub unique { + my %opts = (f=>250.0, q=>5, r=>2, a=>1, b=>3); + getopts('Qf:q:r:a:b:m', \%opts); + die("Usage: samtools.pl unique [-f $opts{f}] \n") if (@ARGV == 0 && -t STDIN); + my $last = ''; + my $recal_Q = !defined($opts{Q}); + my $multi_only = defined($opts{m}); + my @a; while (<>) { - my @t = split; - if ($t[2] eq '*') { + 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 = (); +} + +# +# uniqcmp: compare two SAM files +# + +sub uniqcmp { + my %opts = (q=>10, s=>100); + getopts('pq:s:', \%opts); + die("Usage: samtools.pl uniqcmp \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 { - my $q = $t[$col]; - $q = 99 if ($q > 99); - $q = int($q/10); - my $is_het = ($t[3] =~ /^[ACGT]$/)? 0 : 1; - ++$cnt[$q][$is_het]; - $hash{$t[0],$t[1]} = $q; + print STDERR "$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); +} + +sub plp2vcf { + while (<>) { + my @t = split; + next if ($t[3] eq '*/*'); + if ($t[2] eq '*') { # indel + my @s = split("/", $t[3]); + my (@a, @b); + my ($ref, $alt); + for (@s) { + next if ($_ eq '*'); + if (/^-/) { + push(@a, 'N'.substr($_, 1)); + push(@b, 'N'); + } elsif (/^\+/) { + push(@a, 'N'); + push(@b, 'N'.substr($_, 1)); + } + } + if ($a[0] && $a[1]) { + if (length($a[0]) < length($a[1])) { + $ref = $a[1]; + $alt = ($b[0] . ('N' x (length($a[1]) - length($a[0])))) . ",$b[1]"; + } elsif (length($a[0]) > length($a[1])) { + $ref = $a[0]; + $alt = ($b[1] . ('N' x (length($a[0]) - length($a[1])))) . ",$b[0]"; + } else { + $ref = $a[0]; + $alt = ($b[0] eq $b[1])? $b[0] : "$b[0],$b[1]"; + } + } else { + $ref = $a[0]; $alt = $b[0]; + } + print join("\t", @t[0,1], '.', $ref, $alt, $t[5], '.', '.'), "\n"; + } else { # SNP } } }