--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lib/CPT/Writer/Fasta.pm	Mon Jun 05 02:47:24 2023 +0000
@@ -0,0 +1,78 @@
+package CPT::Writer::Fasta;
+use Moose;
+with 'CPT::Writer';
+require Bio::SeqIO;
+
+sub process {
+	my ($self) = @_;
+	$self->processed_data( $self->data );
+	$self->processing_complete(1);
+	return 1;
+}
+
+sub write {
+	my ($self) = @_;
+	if ( $self->processing_complete ) {
+		$self->OutputFilesClass->extension( $self->suffix() );
+		my $next_output_file = $self->OutputFilesClass->get_next_file();
+		open( my $filehandle, '>', $next_output_file );
+		# This is probably a good change but will need testing.
+		if ( ref( $self->processed_data )  eq 'Bio::PrimarySeqI') {
+			my $outseq = Bio::SeqIO->new(
+				-fh     => $filehandle,
+				-format => 'Fasta',
+			);
+			$outseq->write_seq( $self->processed_data );
+		}
+		elsif ( ref( $self->processed_data )  eq 'ARRAY') {
+			my $outseq = Bio::SeqIO->new(
+				-fh     => $filehandle,
+				-format => 'Fasta',
+			);
+			foreach my $seq (@{$self->processed_data()}){
+				$outseq->write_seq( $seq );
+			}
+		}
+		else {
+			print $filehandle $self->processed_data;
+		}
+		close($filehandle);
+	}
+	else {
+		warn "Write called but processing was not marked as complete. Not writing";
+	}
+}
+
+sub suffix {
+	return 'fa';
+}
+no Moose;
+1;
+
+__END__
+
+=pod
+
+=encoding UTF-8
+
+=head1 NAME
+
+CPT::Writer::Fasta
+
+=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