--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lib/CPT/Bio/GFF_Parsing.pm	Mon Jun 05 02:47:24 2023 +0000
@@ -0,0 +1,89 @@
+package CPT::Bio::GFF_Parsing;
+use Moose;
+use autodie;
+
+my $tags = 'allele anticodon artificial_location
+bio_material bound_moiety cell_line cell_type chromosome citation
+clone clone_lib codon_start collected_by collection_date compare
+country cultivar culture_collection db_xref dev_stage direction
+EC_number ecotype environmental_sample estimated_length exception
+experiment focus frequency function gap_type gene gene_synonym
+germline haplogroup haplotype host identified_by inference isolate
+isolation_source lab_host lat_lon linkage_evidence locus_tag
+macronuclear map mating_type mobile_element_type mod_base mol_type
+ncRNA_class note number old_locus_tag operon organelle organism
+partial PCR_conditions PCR_primers phenotype plasmid pop_variant
+product protein_id proviral pseudo rearranged replace
+ribosomal_slippage rpt_family rpt_type rpt_unit_range rpt_unit_seq
+satellite segment serotype serovar sex specimen_voucher
+standard_name strain sub_clone sub_species sub_strain tag_peptide
+tissue_lib tissue_type transgenic translation transl_except
+transl_table trans_splicing variety';
+my %valid_tags = map { $_ => 1 } split( /\s+/, $tags );
+
+my $keys = "-10_signal -35_signal 3'UTR 5'UTR
+CAAT_signal CDS C_region D-loop D_segment GC_signal J_segment LTR
+N_region RBS STS S_region TATA_signal V_region V_segment
+assembly_gap attenuator enhancer exon gap gene iDNA intron mRNA
+mat_peptide misc_RNA misc_binding misc_difference misc_feature
+misc_recomb misc_signal misc_structure mobile_element
+modified_base ncRNA old_sequence operon oriT polyA_signal
+polyA_site precursor_RNA prim_transcript primer_bind promoter
+protein_bind rRNA rep_origin repeat_region sig_peptide source
+stem_loop tRNA terminator tmRNA transit_peptide unsure variation";
+my %valid_keys = map { $_ => 1 } split( /\s+/, $keys );
+
+has 'tag_conv' => ( is => 'ro', isa => 'HashRef', default => sub { return {
+	#tags
+	'dbxref'   => 'db_xref',
+	'parent'   => 'note',
+	'name'     => 'label',
+	'Name'     => 'label',
+	'old-name' => 'obsolete_name',
+	'id'       => 'note',
+	'nat-host' => 'host',
+	'genome'   => 'note',
+	'region'   => 'source',
+}; });
+
+
+sub fix_gff_tag {
+	my ($self, $tag) = @_;
+	# Lowercase it
+	if(defined $tag && defined(${$self->tag_conv()}{lc($tag)})){
+		return ${$self->tag_conv()}{lc($tag)};
+	}
+	return $tag;
+}
+
+
+no Moose;
+1;
+
+__END__
+
+=pod
+
+=encoding UTF-8
+
+=head1 NAME
+
+CPT::Bio::GFF_Parsing
+
+=head1 VERSION
+
+version 1.99.4
+
+=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