+my %alias_reverse;
+
for my $file_name (@ARGV) {
my $file = new IO::File $file_name, 'r' or die "Unable to open file $file_name $!";
while (<$file>) {
next if /^"Name"/;
my @gene = map {s/^\"//; s/\"$//; $_;} split /(?<=\")\,(?=\")/, $_;
+ # check to see if there's a different name we should be using
+ if (not exists $genes{$gene[NAME]}) {
+ # if the gene has a valid name, we do at least one test.
+ my $num_tested = $gene[NAME] ne 'NO NAME' ? 1 : 0;
+ my %candidates;
+ if ($gene[NAME] ne 'NO NAME' and exists $alias_reverse{$gene[NAME]} and $alias_reverse{$gene[NAME]} ne '') {
+ $candidates{$alias_reverse{$gene[NAME]}}++;
+ }
+ else {
+ for my $alias (grep {$_ !~ /^NO (ALIASES|NAME)$/} split(/; /, $gene[ALIAS])) {
+ if (exists $alias_reverse{$alias} and $alias_reverse{$alias} ne '') {
+ $candidates{$alias_reverse{$alias}}++;
+ }
+ $num_tested++;
+ }
+ }
+ #print STDERR "Choosing $alias_reverse{$gene[NAME]} for $gene[NAME]\n";
+ for my $candidate (keys %candidates) {
+ if ($candidates{$candidate} > ($num_tested/2)) {
+ print STDERR "Choosing $candidate for '$gene[NAME]', as it matched $candidates{$candidate} of $num_tested tests\n";
+ $gene[NAME] = $candidate;
+ }
+ }
+ }
$genes{$gene[NAME]}{name} = $gene[NAME];
$genes{$gene[NAME]}{database}{$gene[DBNAME]}++;
$genes{$gene[NAME]}{hits}++;
add_if_better($genes{$gene[NAME]},'description',$gene[DESCRIPTION]);
add_if_better($genes{$gene[NAME]},'location',$gene[LOCATION]);
add_unique_parts($genes{$gene[NAME]},'function',split(/; /, $gene[FUNCTION]));
- add_unique_parts($genes{$gene[NAME]},'alias', split(/; /, $gene[ALIAS]));
+ my @aliases = grep {$_ ne 'NO ALIASES'} split(/; /, $gene[ALIAS]);
+ add_unique_parts($genes{$gene[NAME]},'alias', @aliases);
+ if ($gene[NAME] ne 'NO NAME') {
+ for my $alias (@aliases) {
+ if (not exists $alias_reverse{$alias}) {
+ $alias_reverse{$alias} = $gene[NAME];
+ }
+ elsif ($alias_reverse{$alias} ne $gene[NAME]) {
+ print STDERR "Alias $alias for $gene[NAME] also points at $alias_reverse{$alias} [".join(',',@aliases).".]\n";
+ $alias_reverse{$alias} = '';
+ }
+ }
+ }
}
}
$auto_weight{$keyword} = $results_by_this_keyword/$results_combined;
}
+my $max_weight = max(values %auto_weight);
+for my $keyword (keys %auto_weight) {
+ $auto_weight{$keyword} = $auto_weight{$keyword}/$max_weight;
+}
+
print {$results_fh} join(',',map {qq("$_")} @csv_fields),qq(\n);
for my $gene (keys %genes) {
$genes{$gene}{rzscore} = scalar grep {$_ !~ /\[/} keys %{$genes{$gene}{terms}};
$$hr{$key} = [@values];
}
else {
+ return unless @values;
my %temp_hash;
@temp_hash{@{$$hr{$key}}} = (1) x scalar @{$$hr{$key}};
$temp_hash{@values} = (1) x scalar @values;