diff PedToFasta/Ped2Fasta.pl @ 1:420b57c3c185 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PedToFasta/Ped2Fasta.pl	Fri Jul 10 04:39:30 2015 -0400
@@ -0,0 +1,70 @@
+
+#!/usr/bin/perl
+
+use strict;
+use Getopt::Long;
+
+my $usage = qq~Usage:$0 <args> [<opts>]
+
+where <args> are:
+
+    -i, --in           <PED input>
+    -o, --out          <Fasta output>
+~;
+$usage .= "\n";
+
+my ($input,$out);
+
+
+
+GetOptions(
+	"in=s"          => \$input,
+	"out=s"          => \$out,
+);
+
+
+die $usage
+  if ( !$input || !$out);
+  
+
+my %IUPAC =
+(
+	'00'=> "?",
+	'AA'=> "A",
+	'CC'=> "C",
+	'GG'=> "G",
+	'TT'=> "T",
+        'AG'=> "R",
+        'GA'=> "R",
+        'CT'=> "Y",
+        'TC'=> "Y",
+        'TG'=> "K",
+        'GT'=> "K",
+        'CG'=> "S",
+        'GC'=> "S",
+        'AT'=> "W",
+        'TA'=> "W",
+        'AC'=> "M",
+        'CA'=> "M",
+);
+
+open(my $O,">$out");
+open(my $P,$input) or die "File does not exist";
+while(<$P>)
+{
+	my $line = $_;
+	$line =~s/\r//g;
+	$line =~s/\n//g;
+	my @infos = split("\t",$_);
+	my $ind = $infos[0];
+	print $O ">$ind\n";
+	for (my $i = 6; $i <= $#infos; $i= $i+2)
+	{
+		my $code = $infos[$i].$infos[$i+1];
+		my $letter = $IUPAC{$code};
+		print $O $letter;
+	}
+	print $O "\n";
+}
+close($P);
+close($O);