diff split.pl @ 0:efd5c022b54d draft

planemo upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/split.pl	Mon Apr 09 12:27:49 2018 -0400
@@ -0,0 +1,52 @@
+#!/usr/bin/perl
+
+
+ if($ARGV[0] eq "" || $ARGV[1] eq ""){
+	die "\n\t Usage : perl <thisScript.pl> <file to be split> <number of partitions> \n\n";
+ }
+
+
+ $homfile = $ARGV[0];
+ $numOfFiles = $ARGV[1];
+
+
+ system("grep -c '^>' $homfile > out");
+ open IN, "out" || die "File not found - 2\n";
+ $numOfSeqs = <IN>;
+ close IN; 
+
+ print "Number of seqs is $numOfSeqs\n";
+ my $numPerFile = $numOfSeqs/$numOfFiles;
+ print "Num per File is $numPerFile\n";
+
+ open IN, $homfile || die "File not found - 1\n";
+ $lineIn = <IN>; 
+
+ for($i = 1; $i <= $numOfFiles; $i++){
+	print "$i\n";
+	open FILE, ">".$homfile.".".$i || die "Can't open file";
+	print FILE $lineIn;
+	$seqs = 1;
+        $lineIn = <IN>;
+	while(defined $lineIn && $seqs < $numPerFile){
+ 		print FILE $lineIn;
+		if ($lineIn =~ /^>/) { $seqs++; }
+		$lineIn = <IN>;
+	}
+	while(defined $lineIn && $lineIn !~ /^>/){
+		print FILE $lineIn;
+		$lineIn = <IN>;
+	}
+	close FILE;
+ }
+ $i = $i -1;
+ open FILE, ">>".$homfile.".".$i;
+ while ($lineIn = <IN>){
+	print FILE $lineIn;
+ }
+ close FILE;
+
+ close IN;
+
+
+