comparison PsiCLASS-1.0.2/samtools-0.1.19/misc/bowtie2sam.pl @ 0:903fc43d6227 draft default tip

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author lsong10
date Fri, 26 Mar 2021 16:52:45 +0000
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1 #!/usr/bin/perl -w
2
3 # Contact: lh3
4 # Version: 0.1.1
5
6 use strict;
7 use warnings;
8 use Getopt::Std;
9
10 &bowtie2sam;
11 exit;
12
13 sub bowtie2sam {
14 my %opts = ();
15 die("Usage: bowtie2sam.pl <aln.bowtie>\n") if (@ARGV == 0 && -t STDIN);
16 # core loop
17 my (@s, $last, @staging, $k, $best_s, $subbest_s, $best_k);
18 $last = '';
19 while (<>) {
20 my ($name, $nm) = &bowtie2sam_aux($_, \@s); # read_name, number of mismatches
21 if ($name eq $last) {
22 # I do not know whether the multiple hits are ordered on the
23 # number of mismatches. I assume they are not and so I have to
24 # keep all these multiple hits in memory.
25 @{$staging[$k]} = @s;
26 if ($best_s > $nm) {
27 $subbest_s = $best_s;
28 $best_s = $nm;
29 $best_k = $k;
30 } elsif ($subbest_s > $nm) {
31 $subbest_s = $nm;
32 }
33 ++$k;
34 } else {
35 if ($last) {
36 if ($best_s == $subbest_s) {
37 $staging[$best_k][4] = 0;
38 } elsif ($subbest_s - $best_s == 1) {
39 $staging[$best_k][4] = 15 if ($staging[$best_k][4] > 15);
40 }
41 print join("\t", @{$staging[$best_k]}), "\n";
42 }
43 $k = 1; $best_s = $nm; $subbest_s = 1000; $best_k = 0;
44 @{$staging[0]} = @s;
45 $last = $name;
46 }
47 }
48 print join("\t", @{$staging[$best_k]}), "\n" if ($best_k >= 0);
49 }
50
51 sub bowtie2sam_aux {
52 my ($line, $s) = @_;
53 chomp($line);
54 my @t = split("\t", $line);
55 my $ret;
56 @$s = ();
57 # read name
58 $s->[0] = $ret = $t[0];
59 $s->[0] =~ s/\/[12]$//g;
60 # initial flag (will be updated later)
61 $s->[1] = 0;
62 # read & quality
63 $s->[9] = $t[4]; $s->[10] = $t[5];
64 # cigar
65 $s->[5] = length($s->[9]) . "M";
66 # coor
67 $s->[2] = $t[2]; $s->[3] = $t[3] + 1;
68 $s->[1] |= 0x10 if ($t[1] eq '-');
69 # mapQ
70 $s->[4] = $t[6] == 0? 25 : 0;
71 # mate coordinate
72 $s->[6] = '*'; $s->[7] = $s->[8] = 0;
73 # aux
74 my $nm = @t - 7;
75 push(@$s, "NM:i:" . (@t-7));
76 push(@$s, "X$nm:i:" . ($t[6]+1));
77 my $md = '';
78 if ($t[7]) {
79 $_ = $t[7];
80 my $a = 0;
81 while (/(\d+):[ACGTN]>([ACGTN])/gi) {
82 my ($y, $z) = ($1, $2);
83 $md .= (int($y)-$a) . $z;
84 $a += $y - $a + 1;
85 }
86 $md .= length($s->[9]) - $a;
87 } else {
88 $md = length($s->[9]);
89 }
90 push(@$s, "MD:Z:$md");
91 return ($ret, $nm);
92 }