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|
#!/usr/bin/perl
#-------------------------------------------------------------------------------
#
# Find variants having either:
#
# 1) EFF impact HIGH
#
# 2) EFF impact MODERATE and NEXT_PROT impact HIGH
#
#
# Pablo Cingolani
#-------------------------------------------------------------------------------
# Debug mode?
$debug=0;
# Effect impact coded as number
$MODERATE = 1;
$HIGH = 2;
#-------------------------------------------------------------------------------
# Funciton max
#-------------------------------------------------------------------------------
sub max($$) {
my($a,$b) = @_;
if( $a >= $b ) { return $a; }
return $b;
}
#-------------------------------------------------------------------------------
# Main
#-------------------------------------------------------------------------------
# Read STDIN
while( $l = <STDIN> ) {
# Always show VCF headers
if( $l =~ /^#/ ) {
print $l;
} else {
# Split VCF entry
@t = split /\t/, $l;
# Get INFO field
$info = $t[7];
print "INFO: $info\n" if $debug;
# Parse INFO field: Get EFF tag
$eff = '';
@infos = split /;/, $info;
foreach $info ( @infos ) {
if( $info =~ /^EFF=(.*)/ ) { $eff = $1; }
}
# Parse EFF tag
if( $eff ne '' ) {
@effs = split /,/, $eff;
# Try to find : ( EFF HIGH ) or ( EFF MODERATE + one NEXT_PROT HIGH )
$effBest = 0;
$nextprotBest = '';
foreach $f ( @effs ) {
# Nextprot effect?
if( $f =~/^NEXT_PROT/ ) {
if( $f =~ /\(HIGH/ ) { # We only care about high impact nextprot effects
print "NEXT_PROT: $f\n" if $debug;
$nextprotBest = $f;
}
} else {
# Effect (not nextprot)
if( $f =~ /\(HIGH/ ) {
$effBest = max($effBest, $HIGH);
print "EFF : $effBest\t$f\n" if $debug;
} elsif( $f =~ /\(MODERATE/ ) {
$effBest = max($effBest, $MODERATE);
print "EFF : $effBest\t$f\n" if $debug;
}
}
}
# Do we have at least one Moderate EFFect AND one High NEXT_PROT?
if( ($effBest == $HIGH) || (($effBest == $MODERATE) && ($nextprotBest ne '')) ) {
print "$effBest\t$nextprotBest\t" if $debug;
print "$l";
}
}
}
}
|
