X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=misc%2Fsamtools.pl;h=e6dd8e8eac12e659ea0ec12e5bb4ca0572252ed1;hb=6ad0dc55ff3abf908a99935321ff8fa5efed4d88;hp=0b0e9d2d378e4a5965c2ecea9a4c570fa6983112;hpb=f87674c1c5924b5731aa86ac849553d1b44e52de;p=samtools.git diff --git a/misc/samtools.pl b/misc/samtools.pl index 0b0e9d2..e6dd8e8 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 $command = shift(@ARGV); -my %func = (showALEN=>\&showALEN, pileup2fq=>\&pileup2fq, varFilter=>\&varFilter, unique=>\&unique); +my %func = (showALEN=>\&showALEN, pileup2fq=>\&pileup2fq, varFilter=>\&varFilter, + unique=>\&unique, uniqcmp=>\&uniqcmp, sra2hdr=>\&sra2hdr, sam2fq=>\&sam2fq); die("Unknown command \"$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..$#t]), "\n"; } } @@ -35,9 +37,19 @@ sub showALEN { # varFilter # +# +# Filtration code: +# +# d low depth +# D high depth +# W too many SNPs in a window (SNP only) +# G close to a high-quality indel (SNP only) +# Q low RMS mapping quality (SNP only) +# g close to another indel with higher quality (indel only) + sub varFilter { my %opts = (d=>3, D=>100, l=>30, Q=>25, q=>10, G=>25, s=>100, w=>10, W=>10, N=>2, p=>undef); - getopts('pd:D:l:Q:w:W:N:G:', \%opts); + getopts('pq:d:D:l:Q:w:W:N:G:', \%opts); die(qq/ Usage: samtools.pl varFilter [options] @@ -65,7 +77,7 @@ Options: -Q INT minimum RMS mapping quality for SNPs [$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 >= $t[1]); @@ -214,21 +226,120 @@ sub p2q_print_str { } } +# +# sam2fq +# + +sub sam2fq { + my %opts = (n=>20, p=>''); + getopts('n:p:', \%opts); + die("Usage: samtools.pl sam2fq [-n 20] [-p ] \n") if (@ARGV == 0 && -t STDIN); + if ($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 +# + +# 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=>5.0, q=>5, r=>2, a=>1, b=>3); - getopts('f:', \%opts); + 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 $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); @@ -237,19 +348,19 @@ sub unique { $cigar =~ s/(\d+)M/$mm+=$1/eg; $score = $mm * $opts{a} - $go * $opts{q} - $ge * $opts{r}; # no mismatches... } - $score = 0 if ($score < 0); + $score = 1 if ($score < 1); if ($t[0] ne $last) { - &unique_aux(\@a, $opts{f}) if (@a); + &unique_aux(\@a, $opts{f}, $recal_Q, $multi_only) if (@a); $last = $t[0]; } push(@a, [$score, \@t]); } - &unique_aux(\@a, $opts{f}) if (@a); + &unique_aux(\@a, $opts{f}, $recal_Q, $multi_only) if (@a); } sub unique_aux { - my ($a, $fac) = @_; - my ($max, $max2, $max_i) = (-1, -1, -1); + my ($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; @@ -257,12 +368,88 @@ sub unique_aux { $max2 = $a->[$i][0]; } } - my $q = int($fac * ($max - $max2) + .499); - $a->[$max_i][1][4] = $q < 250? $q : 250; + if ($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] >= $opts{q}); + } else { + print STDERR "$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 #