--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/snpEff_2_1a/scripts/vcfEffOnePerLine.pl	Fri Apr 20 14:47:09 2012 -0400
@@ -0,0 +1,53 @@
+#!/usr/bin/perl
+
+#-------------------------------------------------------------------------------
+#
+# Read a VCF file (via STDIN), split EFF fields from INFO column into many lines
+# leaving one line per effect.
+#
+# Note: In lines having multiple effects, all other information will be 
+#       repeated. Only the 'EFF' field will change.
+#
+#															Pablo Cingolani 2012
+#-------------------------------------------------------------------------------
+
+$INFO_FIELD_NUM = 7;
+
+while( $l = <STDIN> ) {
+	# Show header lines
+	if( $l =~ /^#/ ) { print $l; }	
+	else {
+		chomp $l;
+
+		@t = @infos = @effs = (); # Clear arrays
+
+		# Non-header lines: Parse fields
+		@t = split /\t/, $l;
+
+		# Get INFO column
+		$info = $t[ $INFO_FIELD_NUM ];
+
+		# Parse INFO column 
+		@infos = split /;/, $info;
+
+		# Find EFF field
+		$infStr = "";
+		foreach $inf ( @infos ) {
+			# Is this the EFF field? => Find it and split it
+			if( $inf =~/^EFF=(.*)/ ) { @effs = split /,/, $1; }
+			else { $infStr .= ( $infStr eq '' ? '' : ';' ) . $inf; }
+		}	
+
+		# Print VCF line
+		if( $#effs <= 0 )	{ print "$l\n"; }	# No EFF found, just show line
+		else {
+			$pre = "";
+			for( $i=0 ; $i < $INFO_FIELD_NUM ; $i++ ) { $pre .= ( $i > 0 ? "\t" : "" ) . "$t[$i]"; }
+
+			$post = "";
+			for( $i=$INFO_FIELD_NUM+1 ; $i <= $#t ; $i++ ) { $post .= "\t$t[$i]"; }
+
+			foreach $eff ( @effs ) { print $pre . "\t" . $infStr . ( $infStr eq '' ? '' : ';' ) . "EFF=$eff" . $post . "\n" ; }
+		}
+	}
+}