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comparison PedToFasta/Ped2Fasta.pl @ 9:98c37a5d67f4 draft

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author dereeper
date Wed, 07 Feb 2018 22:08:47 -0500
parents 420b57c3c185
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8:6bf69b40365c 9:98c37a5d67f4
1
2 #!/usr/bin/perl
3
4 use strict;
5 use Getopt::Long;
6
7 my $usage = qq~Usage:$0 <args> [<opts>]
8
9 where <args> are:
10
11 -i, --in <PED input>
12 -o, --out <Fasta output>
13 ~;
14 $usage .= "\n";
15
16 my ($input,$out);
17
18
19
20 GetOptions(
21 "in=s" => \$input,
22 "out=s" => \$out,
23 );
24
25
26 die $usage
27 if ( !$input || !$out);
28
29
30 my %IUPAC =
31 (
32 '00'=> "?",
33 'AA'=> "A",
34 'CC'=> "C",
35 'GG'=> "G",
36 'TT'=> "T",
37 'AG'=> "R",
38 'GA'=> "R",
39 'CT'=> "Y",
40 'TC'=> "Y",
41 'TG'=> "K",
42 'GT'=> "K",
43 'CG'=> "S",
44 'GC'=> "S",
45 'AT'=> "W",
46 'TA'=> "W",
47 'AC'=> "M",
48 'CA'=> "M",
49 );
50
51 open(my $O,">$out");
52 open(my $P,$input) or die "File does not exist";
53 while(<$P>)
54 {
55 my $line = $_;
56 $line =~s/\r//g;
57 $line =~s/\n//g;
58 my @infos = split("\t",$_);
59 my $ind = $infos[0];
60 print $O ">$ind\n";
61 for (my $i = 6; $i <= $#infos; $i= $i+2)
62 {
63 my $code = $infos[$i].$infos[$i+1];
64 my $letter = $IUPAC{$code};
65 print $O $letter;
66 }
67 print $O "\n";
68 }
69 close($P);
70 close($O);