diff tools/filters/cutWrapper.pl @ 0:9071e359b9a3

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/filters/cutWrapper.pl	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,77 @@
+#!/usr/bin/perl -w
+
+use strict;
+use warnings;
+
+my @columns = ();
+my $del = "";
+my @in = ();
+my @out = ();
+my $command = "";
+my $field = 0;
+
+# a wrapper for cut for use in galaxy
+# cutWrapper.pl [filename] [columns] [delim] [output]
+
+die "Check arguments\n" unless @ARGV == 4;
+
+$ARGV[1] =~ s/\s+//g;
+foreach ( split /,/, $ARGV[1] ) {
+  if (m/^c\d{1,}$/i) {
+    push (@columns, $_);
+    $columns[@columns-1] =~s/c//ig;
+  }
+}
+
+die "No columns specified, columns are not preceded with 'c', or commas are not used to separate column numbers: $ARGV[1]\n" if @columns == 0;
+
+my $column_delimiters_href = {
+  'T' => q{\t},
+  'C' => ",",
+  'D' => "-",
+  'U' => "_",
+  'P' => q{\|},
+  'Dt' => q{\.},
+  'Sp' => q{\s+}
+};
+
+$del = $column_delimiters_href->{$ARGV[2]};
+
+open (OUT, ">$ARGV[3]") or die "Cannot create $ARGV[2]:$!\n";
+open (IN,  "<$ARGV[0]") or die "Cannot open $ARGV[0]:$!\n";
+
+while (my $line=<IN>) {
+   if ($line =~ /^#/) {
+     #Ignore comment lines
+   } else {
+     chop($line);
+     @in = split(/$del/, $line);
+     foreach $field (@columns) {
+       if (defined($in[$field-1])) {
+         push(@out, $in[$field-1]);
+       } else {
+         push(@out, ".");
+       }
+     }    
+     print OUT join("\t",@out), "\n";
+     @out = ();
+   }
+}
+
+#while (<IN>) {
+#  chop;
+#  @in = split /$del/; 
+#  foreach $field (@columns) {
+#    if (defined($in[$field-1])) {
+#      push(@out, $in[$field-1]);
+#    } else {
+#      push(@out, ".");
+#    }
+#  }
+#  print OUT join("\t",@out), "\n";
+#  @out = ();
+#}
+close IN;
+
+close OUT;
+