X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=misc%2Fsamtools.pl;h=86b285c5fa6c144a1d60ed61cb48a23bde7f134f;hp=c014c52bcf0880d39ba23f567a31396017220142;hb=4a17fa7e1f91b2fe04ad334a63fc2b0d5e859d8a;hpb=b27e00385f41769d03a8cca4dbd71275fc9fa906 diff --git a/misc/samtools.pl b/misc/samtools.pl index c014c52..86b285c 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 $command = shift(@ARGV); -my %func = (showALEN=>\&showALEN, pileup2fq=>\&pileup2fq, varFilter=>\&varFilter); +my %func = (showALEN=>\&showALEN, pileup2fq=>\&pileup2fq, varFilter=>\&varFilter, + unique=>\&unique, uniqcmp=>\&uniqcmp); die("Unknown command \"$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..$#t]), "\n"; } } @@ -37,7 +39,7 @@ sub showALEN { sub varFilter { my %opts = (d=>3, D=>100, l=>30, Q=>25, q=>10, G=>25, s=>100, w=>10, W=>10, N=>2, p=>undef); - getopts('pd:D:l:Q:w:W:N:G:', \%opts); + getopts('pq:d:D:l:Q:w:W:N:G:', \%opts); die(qq/ Usage: samtools.pl varFilter [options] @@ -65,7 +67,7 @@ Options: -Q INT minimum RMS mapping quality for SNPs [$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]); @@ -215,27 +217,128 @@ sub p2q_print_str { } # -# varStats +# unique # -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; +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}] \n") if (@ARGV == 0 && -t STDIN); + my $last = ''; + my $recal_Q = !defined($opts{Q}); + 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) 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 \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); } #