convert NCBI-BLASTN to SAM

diff --git a/misc/blast2sam.pl b/misc/blast2sam.pl
new file mode 100755 (executable)
index 0000000..084f018
--- /dev/null
+++ b/misc/blast2sam.pl
@@ -0,0 +1,92 @@
+#!/usr/bin/perl -w
+
+use strict;
+use warnings;
+use Getopt::Std;
+
+&blast2sam;
+
+sub blast2sam {
+  my %opts = ();
+  getopts('s', \%opts);
+  die("Usage: blast2sam.pl <in.blastn>\n") if (-t STDIN && @ARGV == 0);
+  my ($qlen, $slen, $q, $s, $qbeg, $qend, @sam, @cigar, @cmaux, $show_seq);
+  $show_seq = defined($opts{s});
+  @sam = (); @sam[0,4,6..8,10] = ('', 255, '*', 0, 0, '*');
+  while (<>) {
+       if (@cigar && (/^Query=/ || /Score =.*bits.*Expect/)) { # print
+         &blast_print_sam(\@sam, \@cigar, \@cmaux, $qlen - $qend);
+         @cigar = ();
+       }
+       if (/^Query= (\S+)/) {
+         $sam[0] = $1;
+       } elsif (/\((\S+)\s+letters\)/) {
+         $qlen = $1; $qlen =~ s/,//g;
+       } elsif (/^>(\S+)/) {
+         $sam[2] = $1;
+       } elsif (/Length = (\d+)/) {
+         $slen = $1;
+       } elsif (/Score =\s+(\S+) bits.+Expect(\(\d+\))? = (\S+)/) { # the start of an alignment block
+         my ($as, $ev) = (int($1 + .499), $3);
+         $ev = "1$ev" if ($ev =~ /^e/);
+         @sam[1,3,9,11,12] = (0, 0, '', "AS:i:$as", "EV:Z:$ev");
+         @cigar = (); $qbeg = 0;
+         @cmaux = (0, 0, 0, '');
+       } elsif (/Strand = (\S+) \/ (\S+)/) {
+         $sam[1] |= 0x10 if ($2 eq 'Minus');
+       } elsif (/Query\:\s(\d+)\s*(\S+)\s(\d+)/) {
+         $q = $2;
+         unless ($qbeg) {
+               $qbeg = $1;
+               push(@cigar, ($1-1) . "H") if ($1 > 1);
+         }
+         $qend = $3;
+         if ($show_seq) {
+               my $x = $q;
+               $x =~ s/-//g; $sam[9] .= $x;
+         }
+       } elsif (/Sbjct\:\s(\d+)\s*(\S+)\s(\d+)/) {
+         $s = $2;
+         if ($sam[1] & 0x10) {
+               $sam[3] = $3;
+         } else {
+               $sam[3] = $1 unless ($sam[3]);
+         }
+         &aln2cm(\@cigar, \$q, \$s, \@cmaux);
+       }
+  }
+  &blast_print_sam(\@sam, \@cigar, \@cmaux, $qlen - $qend);
+}
+
+sub blast_print_sam {
+  my ($sam, $cigar, $cmaux, $qrest) = @_;
+  push(@$cigar, $cmaux->[1] . substr("MDI", $cmaux->[0], 1));
+  push(@$cigar, $qrest . 'H') if ($qrest);
+  if ($sam->[1] & 0x10) {
+       @$cigar = reverse(@$cigar);
+       $sam->[9] = reverse($sam->[9]);
+       $sam->[9] =~ tr/atgcrymkswATGCRYMKSW/tacgyrkmswTACGYRKMSW/;
+  }
+  $sam->[9] = '*' if (!$sam->[9]);
+  $sam->[5] = join('', @$cigar);
+  print join("\t", @$sam), "\n";
+}
+
+sub aln2cm {
+  my ($cigar, $q, $s, $cmaux) = @_;
+  my $l = length($$q);
+  for (my $i = 0; $i < $l; ++$i) {
+       my $op;
+       # set $op
+       if (substr($$q, $i, 1) eq '-') { $op = 2; }
+       elsif (substr($$s, $i, 1) eq '-') { $op = 1; }
+       else { $op = 0; }
+       # for CIGAR
+       if ($cmaux->[0] == $op) {
+         ++$cmaux->[1];
+       } else {
+         push(@$cigar, $cmaux->[1] . substr("MDI", $cmaux->[0], 1));
+         $cmaux->[0] = $op; $cmaux->[1] = 1;
+       }
+  }
+}