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1 #!/usr/bin/perl -w
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2
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3 use strict;
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4 use warnings;
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5 use Getopt::Std;
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6
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7 &blast2sam;
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8
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9 sub blast2sam {
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10 my %opts = ();
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11 getopts('s', \%opts);
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12 die("Usage: blast2sam.pl <in.blastn>\n") if (-t STDIN && @ARGV == 0);
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13 my ($qlen, $slen, $q, $s, $qbeg, $qend, @sam, @cigar, @cmaux, $show_seq);
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14 $show_seq = defined($opts{s});
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15 @sam = (); @sam[0,4,6..8,10] = ('', 255, '*', 0, 0, '*');
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16 while (<>) {
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17 if (@cigar && (/^Query=/ || /Score =.*bits.*Expect/)) { # print
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18 &blast_print_sam(\@sam, \@cigar, \@cmaux, $qlen - $qend);
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19 @cigar = ();
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20 }
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21 if (/^Query= (\S+)/) {
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22 $sam[0] = $1;
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23 } elsif (/\((\S+)\s+letters\)/) {
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24 $qlen = $1; $qlen =~ s/,//g;
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25 } elsif (/^>(\S+)/) {
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26 $sam[2] = $1;
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27 } elsif (/Length = (\d+)/) {
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28 $slen = $1;
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29 } elsif (/Score =\s+(\S+) bits.+Expect(\(\d+\))? = (\S+)/) { # the start of an alignment block
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30 my ($as, $ev) = (int($1 + .499), $3);
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31 $ev = "1$ev" if ($ev =~ /^e/);
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32 @sam[1,3,9,11,12] = (0, 0, '', "AS:i:$as", "EV:Z:$ev");
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33 @cigar = (); $qbeg = 0;
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34 @cmaux = (0, 0, 0, '');
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35 } elsif (/Strand = (\S+) \/ (\S+)/) {
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36 $sam[1] |= 0x10 if ($2 eq 'Minus');
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37 } elsif (/Query\:\s(\d+)\s*(\S+)\s(\d+)/) {
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38 $q = $2;
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39 unless ($qbeg) {
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40 $qbeg = $1;
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41 push(@cigar, ($1-1) . "H") if ($1 > 1);
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42 }
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43 $qend = $3;
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44 if ($show_seq) {
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45 my $x = $q;
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46 $x =~ s/-//g; $sam[9] .= $x;
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47 }
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48 } elsif (/Sbjct\:\s(\d+)\s*(\S+)\s(\d+)/) {
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49 $s = $2;
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50 if ($sam[1] & 0x10) {
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51 $sam[3] = $3;
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52 } else {
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53 $sam[3] = $1 unless ($sam[3]);
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54 }
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55 &aln2cm(\@cigar, \$q, \$s, \@cmaux);
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56 }
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57 }
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58 &blast_print_sam(\@sam, \@cigar, \@cmaux, $qlen - $qend);
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59 }
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60
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61 sub blast_print_sam {
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62 my ($sam, $cigar, $cmaux, $qrest) = @_;
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63 push(@$cigar, $cmaux->[1] . substr("MDI", $cmaux->[0], 1));
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64 push(@$cigar, $qrest . 'H') if ($qrest);
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65 if ($sam->[1] & 0x10) {
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66 @$cigar = reverse(@$cigar);
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67 $sam->[9] = reverse($sam->[9]);
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68 $sam->[9] =~ tr/atgcrymkswATGCRYMKSW/tacgyrkmswTACGYRKMSW/;
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69 }
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70 $sam->[9] = '*' if (!$sam->[9]);
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71 $sam->[5] = join('', @$cigar);
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72 print join("\t", @$sam), "\n";
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73 }
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74
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75 sub aln2cm {
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76 my ($cigar, $q, $s, $cmaux) = @_;
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77 my $l = length($$q);
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78 for (my $i = 0; $i < $l; ++$i) {
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79 my $op;
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80 # set $op
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81 if (substr($$q, $i, 1) eq '-') { $op = 2; }
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82 elsif (substr($$s, $i, 1) eq '-') { $op = 1; }
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83 else { $op = 0; }
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84 # for CIGAR
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85 if ($cmaux->[0] == $op) {
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86 ++$cmaux->[1];
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87 } else {
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88 push(@$cigar, $cmaux->[1] . substr("MDI", $cmaux->[0], 1));
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89 $cmaux->[0] = $op; $cmaux->[1] = 1;
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90 }
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91 }
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92 }
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