--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lib/CPT/BioData.pm	Mon Jun 05 02:50:07 2023 +0000
@@ -0,0 +1,246 @@
+package CPT::BioData;
+use Moose;
+use strict;
+use warnings;
+use autodie;
+
+has 'dummy_var' => (isa => 'Str', is => 'ro');
+
+my %genbank_feature_tags = (
+	"locus_tag"            => 1,
+	"gene"                 => 1,
+	"product"              => 1,
+	"allele"               => 1,
+	"anticodon"            => 1,
+	"artificial_location"  => 1,
+	"bio_material"         => 1,
+	"bound_moiety"         => 1,
+	"cell_line"            => 1,
+	"cell_type"            => 1,
+	"chromosome"           => 1,
+	"citation"             => 1,
+	"clone"                => 1,
+	"clone_lib"            => 1,
+	"codon_start"          => 1,
+	"collected_by"         => 1,
+	"collection_date"      => 1,
+	"compare"              => 1,
+	"country"              => 1,
+	"cultivar"             => 1,
+	"culture_collection"   => 1,
+	"db_xref"              => 1,
+	"dev_stage"            => 1,
+	"direction"            => 1,
+	"EC_number"            => 1,
+	"ecotype"              => 1,
+	"environmental_sample" => 1,
+	"estimated_length"     => 1,
+	"exception"            => 1,
+	"experiment"           => 1,
+	"focus"                => 1,
+	"frequency"            => 1,
+	"function"             => 1,
+	"gap_type"             => 1,
+	"gene_synonym"         => 1,
+	"germline"             => 1,
+	"haplogroup"           => 1,
+	"haplotype"            => 1,
+	"host"                 => 1,
+	"identified_by"        => 1,
+	"inference"            => 1,
+	"isolate"              => 1,
+	"isolation_source"     => 1,
+	"lab_host"             => 1,
+	"lat_lon"              => 1,
+	"linkage_evidence"     => 1,
+	"macronuclear"         => 1,
+	"map"                  => 1,
+	"mating_type"          => 1,
+	"mobile_element_type"  => 1,
+	"mod_base"             => 1,
+	"mol_type"             => 1,
+	"ncRNA_class"          => 1,
+	"note"                 => 1,
+	"number"               => 1,
+	"old_locus_tag"        => 1,
+	"operon"               => 1,
+	"organelle"            => 1,
+	"organism"             => 1,
+	"partial"              => 1,
+	"PCR_conditions"       => 1,
+	"PCR_primers"          => 1,
+	"phenotype"            => 1,
+	"plasmid"              => 1,
+	"pop_variant"          => 1,
+	"protein_id"           => 1,
+	"proviral"             => 1,
+	"pseudo"               => 1,
+	"rearranged"           => 1,
+	"replace"              => 1,
+	"ribosomal_slippage"   => 1,
+	"rpt_family"           => 1,
+	"rpt_type"             => 1,
+	"rpt_unit_range"       => 1,
+	"rpt_unit_seq"         => 1,
+	"satellite"            => 1,
+	"segment"              => 1,
+	"serotype"             => 1,
+	"serovar"              => 1,
+	"sex"                  => 1,
+	"specimen_voucher"     => 1,
+	"standard_name"        => 1,
+	"strain"               => 1,
+	"sub_clone"            => 1,
+	"sub_species"          => 1,
+	"sub_strain"           => 1,
+	"tag_peptide"          => 1,
+	"tissue_lib"           => 1,
+	"tissue_type"          => 1,
+	"transgenic"           => 1,
+	"translation"          => 1,
+	"transl_except"        => 1,
+	"transl_table"         => 1,
+	"trans_splicing"       => 1,
+	"variety"              => 1,
+);
+my %artemis_colours = (
+	0  => 'rgb(255,255,255)',
+	1  => 'rgb(100,100,100)',
+	2  => 'rgb(255,0,0)',
+	3  => 'rgb(0,255,0)',
+	4  => 'rgb(0,0,255)',
+	5  => 'rgb(0,255,255)',
+	6  => 'rgb(255,0,255)',
+	7  => 'rgb(255,255,0)',
+	8  => 'rgb(152,251,152)',
+	9  => 'rgb(135,206,250)',
+	10 => 'rgb(255,165,0)',
+	11 => 'rgb(200,150,100)',
+	12 => 'rgb(255,200,200)',
+	13 => 'rgb(170,170,170)',
+	14 => 'rgb(0,0,0)',
+	15 => 'rgb(255,63,63)',
+	16 => 'rgb(255,127,127)',
+	17 => 'rgb(255,191,191)',
+);
+
+sub artemis_colour_decode{
+	my ($self, $idx) = @_;
+	return $artemis_colours{$idx};
+}
+
+my %table321 = (
+	'Gly' => 'G', 'Pro' => 'P',
+	'Ala' => 'A',
+	'Val' => 'V',
+	'Leu' => 'L',
+	'Ile' => 'I',
+	'Met' => 'M',
+	'Cys' => 'C',
+	'Phe' => 'F',
+	'Tyr' => 'Y',
+	'Trp' => 'W',
+	'His' => 'H',
+	'Lys' => 'K',
+	'Arg' => 'R',
+	'Gln' => 'Q',
+	'Asn' => 'N',
+	'Glu' => 'E',
+	'Asp' => 'D',
+	'Ser' => 'S',
+	'Thr' => 'T',
+	'XXX' => 'X',
+	'End' => '*',
+	'Stop' => '*'
+);
+
+sub decode321{
+	my ($self, $three) = @_;
+	return $table321{$three};
+}
+
+
+sub get321Table {
+	my ($self) = @_;
+	return \%table321;
+}
+
+
+sub getTranslationTable {
+	my ($self, $table_id) = @_;
+	require Bio::Tools::CodonTable;
+	my $table = Bio::Tools::CodonTable->new( -id => (defined $table_id? $table_id: 1) );
+	my %result;
+	my @codons = qw(A C T G);
+	foreach my $i (@codons) {
+		foreach my $j (@codons) {
+			foreach my $k (@codons) {
+				$result{"$i$j$k"} = $table->translate("$i$j$k");
+			}
+		}
+	}
+	if(defined($table_id) && $table_id == 11){
+		$result{TGA} = '*';
+		$result{TAA} = '#';
+		$result{TAG} = '+';
+	}
+	return \%result;
+}
+
+
+
+sub isValidTag {
+    my ( $self, $tag ) = @_;
+    return $genbank_feature_tags{$tag};
+}
+
+no Moose;
+1;
+
+__END__
+
+=pod
+
+=encoding UTF-8
+
+=head1 NAME
+
+CPT::BioData
+
+=head1 VERSION
+
+version 1.99.4
+
+=head2 get321Table
+
+	$bio->get321Table();
+
+Convenience function which returns a codon translation table (3 letter ID to 1 letter code)
+
+=head2 getTranslationTable
+
+	$bio->getTranslationTable();
+
+Convenience function which returns a hash translated according to Bio::Tools::CodonTable
+
+This is done for speed reasons. CodonTable is very slow and we require better performance
+
+=head2 isValidTag
+
+    if($cptbio->isValidTag('locus_tag')) { ... }
+
+Will validate a GBK feature tag
+
+=head1 AUTHOR
+
+Eric Rasche <rasche.eric@yandex.ru>
+
+=head1 COPYRIGHT AND LICENSE
+
+This software is Copyright (c) 2014 by Eric Rasche.
+
+This is free software, licensed under:
+
+  The GNU General Public License, Version 3, June 2007
+
+=cut