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#!/usr/bin/perl
my $countThreshold = $ARGV[0];
my $localMinProportionThreshold = $ARGV[1];
my $globalMinProportionThreshold = $ARGV[2];
while (<STDIN>) {
chomp;
my ( $id, $bestPcid, @taxonomyEntries ) = split /\t/;
if ( $taxonomyEntries[0] eq "NOPRIMER" ) {
print "$id\t\tNOPRIMER\n";
}
elsif ( $taxonomyEntries[0] eq "NOHIT" ) {
print "$id\t\tNOHIT\n";
}
elsif ( $taxonomyEntries[0] eq "NOMATEPAIR" ) {
print "$id\t\tNOMATEPAIR\n";
}
elsif ( $taxonomyEntries[0] =~ /TOOMANYHITS/ ) {
print "$id\t\tTOOMANYHITS\n";
}
else {
my @newTaxonomyEntries = ();
for my $entry (@taxonomyEntries) {
my (
$label, $numChildren, $count,
$localMinProportion, $localMaxProportion, $globalMinProportion,
$globalMaxProportion, $alternateLocalProportion, $alternateGlobalProportion
) = split /;/, $entry;
if ( $count >= $countThreshold
&& $localMinProportion >= $localMinProportionThreshold
&& $globalMinProportion >= $globalMinProportionThreshold )
{
push @newTaxonomyEntries, $entry;
}
else { last; }
}
#if ( @newTaxonomyEntries == 0 ) {
# push @newTaxonomyEntries, "Root";
#}
# if the trailing entries of the filtered taxonomy string are "SKIP", strip them
while(substr(@newTaxonomyEntries[$#newTaxonomyEntries],0,4) eq "SKIP") { pop @newTaxonomyEntries; }
print "$id\t$bestPcid\t" . ( join "\t", @newTaxonomyEntries ) . "\n";
}
}
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