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#!/usr/bin/perl
#-------------------------------------------------------------------------------
#
# Extract error rates from "SnpEff build" log files
#
#
# Pablo Cingolani 2013
#-------------------------------------------------------------------------------
# Debug mode?
$debug = 0;
# Maximum tolerated error is 2%
$maxError = 2.0;
#-------------------------------------------------------------------------------
# Show error percentage
#-------------------------------------------------------------------------------
sub num($) {
my($num) = @_;
if( $num eq '' ) { return "MISSING\t"; }
elsif( $num > $maxError ) { return sprintf("ERROR\t%.4f%%", $num); }
return sprintf("OK\t%.4f%%", $num);
}
#-------------------------------------------------------------------------------
# Main
#-------------------------------------------------------------------------------
while( $l = <STDIN> ) {
chomp $l;
if( $l =~ /(\S+) check:\s+(\S+).*Error percentage: (.*)%/ ) {
($checkType, $genome, $perc) = ($1, $2, $3);
$err{$genome}->{$checkType} = $perc;
print STDERR "$checkType\t$genome\t$perc\n";
}
}
# Show summary information
print "Genome\tCDS_Check\tError%\tProtein_Check\tError%\n";
foreach $genome ( sort keys %err ) {
printf "%s\t%s\t%s\n", $genome, num($err{$genome}->{'CDS'}), num($err{$genome}->{'Protein'});
}
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