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#!/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;
$l =~ tr/\n\r//d;
@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;
$fieldName = "EFF";
} elsif( $inf =~/^ANN=(.*)/ ) {
@effs = split /,/, $1;
$fieldName = "ANN";
} 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" . ( $infStr eq '' ? '' : ';' ) . "$fieldName=$eff$post\n" ;
}
}
}
}
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