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#!/usr/bin/perl
#-------------------------------------------------------------------------------
#
# Read a BED file (via STDIN), split EFF fields from fourth 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 2013
#-------------------------------------------------------------------------------
$EFF_COLUMN = 3;
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;
# Parse INFO column
@effs = split /;/, $t[ $EFF_COLUMN ];
# Print BED line
if( $#effs <= 0 ) { print "$l\n"; } # No EFF found, just show line
else {
$pre = "";
for( $i=0 ; $i < $EFF_COLUMN ; $i++ ) { $pre .= ( $i > 0 ? "\t" : "" ) . "$t[$i]"; }
$post = "";
for( $i=$EFF_COLUMN+1 ; $i <= $#t ; $i++ ) { $post .= "\t$t[$i]"; }
foreach $eff ( @effs ) { print "$pre\t$eff$post\n"; }
}
}
}
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