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comparison PsiCLASS-1.0.2/samtools-0.1.19/misc/soap2sam.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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-1:000000000000 0:903fc43d6227
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 &soap2sam;
11 exit;
12
13 sub mating {
14 my ($s1, $s2) = @_;
15 my $isize = 0;
16 if ($s1->[2] ne '*' && $s1->[2] eq $s2->[2]) { # then calculate $isize
17 my $x1 = ($s1->[1] & 0x10)? $s1->[3] + length($s1->[9]) : $s1->[3];
18 my $x2 = ($s2->[1] & 0x10)? $s2->[3] + length($s2->[9]) : $s2->[3];
19 $isize = $x2 - $x1;
20 }
21 # update mate coordinate
22 if ($s2->[2] ne '*') {
23 @$s1[6..8] = (($s2->[2] eq $s1->[2])? "=" : $s2->[2], $s2->[3], $isize);
24 $s1->[1] |= 0x20 if ($s2->[1] & 0x10);
25 } else {
26 $s1->[1] |= 0x8;
27 }
28 if ($s1->[2] ne '*') {
29 @$s2[6..8] = (($s1->[2] eq $s2->[2])? "=" : $s1->[2], $s1->[3], -$isize);
30 $s2->[1] |= 0x20 if ($s1->[1] & 0x10);
31 } else {
32 $s2->[1] |= 0x8;
33 }
34 }
35
36 sub soap2sam {
37 my %opts = ();
38 getopts("p", \%opts);
39 die("Usage: soap2sam.pl [-p] <aln.soap>\n") if (@ARGV == 0 && -t STDIN);
40 my $is_paired = defined($opts{p});
41 # core loop
42 my @s1 = ();
43 my @s2 = ();
44 my ($s_last, $s_curr) = (\@s1, \@s2);
45 while (<>) {
46 s/[\177-\377]|[\000-\010]|[\012-\040]//g;
47 next if (&soap2sam_aux($_, $s_curr, $is_paired) < 0);
48 if (@$s_last != 0 && $s_last->[0] eq $s_curr->[0]) {
49 &mating($s_last, $s_curr);
50 print join("\t", @$s_last), "\n";
51 print join("\t", @$s_curr), "\n";
52 @$s_last = (); @$s_curr = ();
53 } else {
54 print join("\t", @$s_last), "\n" if (@$s_last != 0);
55 my $s = $s_last; $s_last = $s_curr; $s_curr = $s;
56 }
57 }
58 print join("\t", @$s_last), "\n" if (@$s_last != 0);
59 }
60
61 sub soap2sam_aux {
62 my ($line, $s, $is_paired) = @_;
63 chomp($line);
64 my @t = split(/\s+/, $line);
65 return -1 if (@t < 9 || $line =~ /^\s/ || !$t[0]);
66 @$s = ();
67 # fix SOAP-2.1.x bugs
68 @t = @t[0..2,4..$#t] unless ($t[3] =~ /^\d+$/);
69 # read name
70 $s->[0] = $t[0];
71 $s->[0] =~ s/\/[12]$//g;
72 # initial flag (will be updated later)
73 $s->[1] = 0;
74 $s->[1] |= 1 | 1<<($t[4] eq 'a'? 6 : 7);
75 $s->[1] |= 2 if ($is_paired);
76 # read & quality
77 $s->[9] = $t[1];
78 $s->[10] = (length($t[2]) > length($t[1]))? substr($t[2], 0, length($t[1])) : $t[2];
79 # cigar
80 $s->[5] = length($s->[9]) . "M";
81 # coor
82 $s->[2] = $t[7]; $s->[3] = $t[8];
83 $s->[1] |= 0x10 if ($t[6] eq '-');
84 # mapQ
85 $s->[4] = $t[3] == 1? 30 : 0;
86 # mate coordinate
87 $s->[6] = '*'; $s->[7] = $s->[8] = 0;
88 # aux
89 push(@$s, "NM:i:$t[9]");
90 my $md = '';
91 if ($t[9]) {
92 my @x;
93 for (10 .. $#t) {
94 push(@x, sprintf("%.3d,$1", $2)) if ($t[$_] =~ /^([ACGT])->(\d+)/i);
95 }
96 @x = sort(@x);
97 my $a = 0;
98 for (@x) {
99 my ($y, $z) = split(",");
100 $md .= (int($y)-$a) . $z;
101 $a += $y - $a + 1;
102 }
103 $md .= length($t[1]) - $a;
104 } else {
105 $md = length($t[1]);
106 }
107 push(@$s, "MD:Z:$md");
108 return 0;
109 }