|
2
|
1 #!/usr/bin/perl
|
|
|
2
|
|
|
3 use strict;
|
|
|
4 use Cwd;
|
|
|
5
|
|
|
6 die qq(
|
|
|
7 Bad numbr of inputs
|
|
|
8
|
|
|
9 ) if(!@ARGV);
|
|
|
10
|
|
|
11 my $options ="";
|
|
|
12 my $file="";
|
|
|
13 my $command="";
|
|
|
14 my $output="";
|
|
|
15 my $working_dir = cwd();
|
|
|
16 my $temp_vcf = "$working_dir/temp";
|
|
|
17 my $log="";
|
|
|
18
|
|
|
19 foreach my $input (@ARGV)
|
|
|
20 {
|
|
|
21 my @tmp = split "::", $input;
|
|
|
22 if($tmp[0] eq "COMMAND")
|
|
|
23 {
|
|
|
24 $command = $tmp[1];
|
|
|
25 }
|
|
|
26 elsif($tmp[0] eq "INPUT")
|
|
|
27 {
|
|
|
28 $file = $tmp[1];
|
|
|
29 }
|
|
|
30 elsif($tmp[0] eq "OPTION")
|
|
|
31 {
|
|
|
32 $options = "$options ${tmp[1]}";
|
|
|
33 }
|
|
|
34 elsif($tmp[0] eq "OUTPUT")
|
|
|
35 {
|
|
|
36 $output = $tmp[1];
|
|
|
37 }
|
|
|
38 elsif($tmp[0] eq "LOG")
|
|
|
39 {
|
|
|
40 $log = $tmp[1];
|
|
|
41 }
|
|
|
42 else
|
|
|
43 {
|
|
|
44 die("Unknown Input: $input\n");
|
|
|
45 }
|
|
|
46 }
|
|
|
47
|
|
|
48 system ("$command $file $options 1>$temp_vcf 2>$log");
|
|
|
49
|
|
|
50 vs2vcf($temp_vcf, $output);
|
|
|
51
|
|
|
52
|
|
|
53 sub vs2vcf
|
|
|
54 {
|
|
|
55
|
|
|
56 #
|
|
|
57 # G l o b a l v a r i a b l e s
|
|
|
58 #
|
|
|
59 my $version = '0.1';
|
|
|
60
|
|
|
61 #
|
|
|
62 # Read in file
|
|
|
63 #
|
|
|
64 my $input = shift;
|
|
|
65 my $output = shift;
|
|
|
66 my $chr_ord = shift;
|
|
|
67 open(IN, $input) or die "Can't open $input': $!\n";
|
|
|
68 open(OUT, ">$output") or die "Can't create $output': $!\n";
|
|
|
69 my %output;
|
|
|
70
|
|
|
71 while ( <IN> )
|
|
|
72 {
|
|
|
73 if ( /^#/ )
|
|
|
74 {
|
|
|
75 print OUT;
|
|
|
76 next;
|
|
|
77 }
|
|
|
78 chomp;
|
|
|
79 my $line = $_;
|
|
|
80
|
|
|
81 my @flds = split ( "\t", $line );
|
|
|
82 my $ref = $flds[3];
|
|
|
83 my $alt = $flds[4];
|
|
|
84 #
|
|
|
85 # Deletion of bases
|
|
|
86 #
|
|
|
87 if ( $alt =~ /^\-/ )
|
|
|
88 {
|
|
|
89 ($flds[3], $flds[4]) = ($ref.substr($alt,1), $ref);
|
|
|
90 }
|
|
|
91
|
|
|
92 #
|
|
|
93 # Insertion of bases
|
|
|
94 #
|
|
|
95 if ( $alt =~ /^\+/ )
|
|
|
96 {
|
|
|
97 $flds[4] = $ref.substr($alt,1);
|
|
|
98 }
|
|
|
99 print OUT join( "\t", @flds),"\n" unless defined $chr_ord;
|
|
|
100 $output{$flds[0]}{$flds[1]} = join( "\t", @flds)."\n" if defined $chr_ord;
|
|
|
101 }
|
|
|
102 close(IN);
|
|
|
103 # if chromosome order given return in sorted order
|
|
|
104 if(defined $chr_ord)
|
|
|
105 {
|
|
|
106 for my $chrom (@{ $chr_ord })
|
|
|
107 {
|
|
|
108 for my $pos (sort {$a<=>$b} keys %{ $output{$chrom} })
|
|
|
109 {
|
|
|
110 print OUT $output{$chrom}{$pos};
|
|
|
111 }
|
|
|
112 }
|
|
|
113 }
|
|
|
114 close(OUT);
|
|
|
115 }
|
|
|
116
|
