--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cpt_psm_comparison_table/lib/CPT/Bio/ORF.pm	Tue Jul 05 05:42:59 2022 +0000
@@ -0,0 +1,205 @@
+package CPT::Bio::ORF;
+use strict;
+use warnings;
+use autodie;
+use Moose;
+
+has min_gene_length => (
+	is          => 'rw',
+	isa         => 'Int',
+	default     => sub {
+		0
+	},
+);
+has sc_atg => ( is => 'rw', isa => 'Bool', default => sub { 1 } );
+has sc_ttg => ( is => 'rw', isa => 'Bool', default => sub { 1 } );
+has sc_ctg => ( is => 'rw', isa => 'Bool', default => sub { 0 } );
+has sc_gtg => ( is => 'rw', isa => 'Bool', default => sub { 1 } );
+
+our %code = (
+	"TTT" => "F", "TTC" => "F", "TTA" => "L", "TTG" => "L", "TCT" => "S",
+	"TCC" => "S", "TCA" => "S", "TCG" => "S", "TAT" => "Y", "TAC" => "Y",
+	"TAA" => "*", "TAG" => "*", "TGT" => "C", "TGC" => "C", "TGA" => "*",
+	"TGG" => "W", "CTT" => "L", "CTC" => "L", "CTA" => "L", "CTG" => "L",
+	"CCT" => "P", "CCC" => "P", "CCA" => "P", "CCG" => "P", "CAT" => "H",
+	"CAC" => "H", "CAA" => "Q", "CAG" => "Q", "CGT" => "R", "CGC" => "R",
+	"CGA" => "R", "CGG" => "R", "ATT" => "I", "ATC" => "I", "ATA" => "I",
+	"ATG" => "M", "ACT" => "T", "ACC" => "T", "ACA" => "T", "ACG" => "T",
+	"AAT" => "N", "AAC" => "N", "AAA" => "K", "AAG" => "K", "AGT" => "S",
+	"AGC" => "S", "AGA" => "R", "AGG" => "R", "GTT" => "V", "GTC" => "V",
+	"GTA" => "V", "GTG" => "V", "GCT" => "A", "GCC" => "A", "GCA" => "A",
+	"GCG" => "A", "GAT" => "D", "GAC" => "D", "GAA" => "E", "GAG" => "E",
+	"GGT" => "G", "GGC" => "G", "GGA" => "G", "GGG" => "G",
+);
+
+
+
+sub run {
+	my ($self, $sequence) = @_;
+	# Read through forward strand
+	my @putative_starts;
+
+	# 30 seconds with a bioperl object
+	# 5 seconds with string munging. >:|
+	my $dna    = uc( $sequence );
+	my $length = length($sequence);
+
+	# Pre-create the regular expressions
+	my ( $regex_forward, $regex_backwards );
+	my $not_statement_f = '^';
+	my $not_statement_r = '^';
+	if ( !$self->sc_atg() ) {
+		$not_statement_f .= 'A';
+		$not_statement_r .= 'T';
+	}
+	if ( !$self->sc_ctg() ) {
+		$not_statement_f .= 'C';
+		$not_statement_r .= 'G';
+	}
+	if ( !$self->sc_ttg() ) {
+		$not_statement_f .= 'T';
+		$not_statement_r .= 'A';
+	}
+	if ( !$self->sc_gtg() ) {
+		$not_statement_f .= 'G';
+		$not_statement_r .= 'C';
+	}
+
+	# If any start is acceptable, we re-add them and remove our ^
+	if($not_statement_r eq '^' && $not_statement_f eq '^'){
+		$not_statement_f = 'ACTG';
+		$not_statement_r = 'ACTG';
+	}
+	$regex_forward   = qr/[${not_statement_f}]TG/;
+	$regex_backwards = qr/CA[${not_statement_r}]/;
+
+	# Collect putative starts
+	for ( my $i = 1 ; $i < $length - 1 ; $i++ ) {
+		my $tri_nt = substr( $dna, $i - 1, 3 );    #$seq_obj->subseq($i,$i+2);
+		if ( $tri_nt =~ $regex_forward ) {
+			push( @putative_starts, [ $i, '+' ] );
+		}
+		if ( $tri_nt =~ $regex_backwards ) {
+			push( @putative_starts, [ $i + 2, '-' ] );
+		}
+	}
+	my %ORFs;
+
+	#Loop through all of the starts we have
+	my $fc = 0;
+	my $rc = 0;
+	foreach (@putative_starts) {
+		my @putative_start = @{$_};
+
+		my $final_seq = "";
+
+		my $add;
+		my $tri_nt;
+		if ( $putative_start[1] eq "+" ) {
+			my $end;
+			for ( my $k = $putative_start[0] ; $k < $length ; $k = $k + 3 )
+			{
+				my $tri_nt = substr( $dna, $k, 3 );
+				my $aa = $code{$tri_nt};
+				if ( $aa && $aa ne '*' ) {
+					$end = $k + 3;
+					$final_seq .= $tri_nt;
+				}
+				else {
+					last;
+				}
+			}
+			if ( length($final_seq)/3 > $self->min_gene_length() ) {
+				$ORFs{ 'f_' + $fc++ } = [
+					length($final_seq)/3,
+					$putative_start[0],
+					$end,
+					'F',
+					$final_seq
+				];
+			}
+		}    # - strand
+		else {
+			my $end;
+			for ( my $k = $putative_start[0] ; $k >= 2 ; $k = $k - 3 ) {
+				my $tmp = reverse( substr( $dna, $k - 3, 3 ) );
+
+				$tmp =~ tr/ACTG/qzAC/;
+				$tmp =~ tr/qz/TG/;
+
+				my $aa = $code{$tmp};
+				if ( defined $aa && $aa ne '*' ) {
+					$end = $k - 1;
+					$final_seq .= $tmp;
+				}
+				else {
+					last;
+				}
+
+			}
+			if ( length($final_seq)/3 > $self->min_gene_length() ) {
+				$ORFs{ 'r_' + $rc++ } = [
+					length($final_seq)/3,
+					$end,
+					$putative_start[0],
+					'R',
+					$final_seq
+				];
+			}
+		}
+	}
+
+	my @orfs;
+
+	for my $orf_key ( sort( keys(%ORFs) ) ) {
+		my @tmp= @{ $ORFs{$orf_key} };
+		my $seqobj = Bio::Seq->new(
+			-display_id => sprintf(
+				'orf%05d_%s',
+				($orf_key + 1), $tmp[3],
+			),
+			-desc => sprintf(
+				'[%s-%s; %s aa long]'
+				,$tmp[1], $tmp[2], $tmp[0]
+			),
+			-seq => $tmp[4]
+		);
+		push(@orfs, $seqobj);
+	}
+	return @orfs;
+}
+
+
+
+no Moose;
+1;
+
+__END__
+
+=pod
+
+=encoding UTF-8
+
+=head1 NAME
+
+CPT::Bio::ORF
+
+=head1 VERSION
+
+version 1.99.4
+
+=function run
+
+=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