--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cpt_psm_recombine/lib/CPT/Writer/Genomic.pm	Tue Jul 05 05:05:13 2022 +0000
@@ -0,0 +1,144 @@
+package CPT::Writer::Genomic;
+use Moose;
+with 'CPT::Writer';
+
+# Specific format of genomic writer
+has 'format' => ( is => 'rw', isa => 'Str', default => 'Genbank');
+
+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 );
+		
+		require Bio::SeqIO;
+		my $obj_type = ref $self->processed_data();
+		if(substr($obj_type,0,10) eq 'Bio::Seq::'){
+			my $outseq = Bio::SeqIO->new(
+				-fh     => $filehandle,
+				-format => $self->format(),
+			);
+			$outseq->write_seq( $self->processed_data );
+		}elsif(substr($obj_type,0,10) eq 'Bio::SeqIO'){
+			my $outseq = Bio::SeqIO->new(
+				-fh     => $filehandle,
+				-format => $self->format(),
+			);
+			while (my $inseq = $self->processed_data()->next_seq()) {
+				$outseq->write_seq($inseq);
+			}
+		}elsif(substr($obj_type,0,8) eq 'Bio::Seq'){
+			my $outseq = Bio::SeqIO->new(
+				-fh     => $filehandle,
+				-format => $self->format(),
+			);
+			$outseq->write_seq( $self->processed_data );
+		}elsif(ref $self->processed_data eq 'ARRAY'){
+			# Assume array of genomes
+			my $outseq = Bio::SeqIO->new(
+				-fh     => $filehandle,
+				-format => $self->format(),
+			);
+			foreach my $inseq(@{$self->processed_data}){
+				$outseq->write_seq($inseq);
+			}
+		}else{
+			print $filehandle $self->processed_data();
+		}
+		close($filehandle);
+	}
+	else {
+		warn
+"Write called but processing was not marked as complete. Not writing";
+	}
+}
+
+sub suffix {
+	my ($self) = @_;
+	my %suffix_map = (
+		'abi'        => 'abi',
+		'ace'        => 'ace',
+		'agave'      => 'agave',
+		'alf'        => 'alf',
+		'asciitree'  => 'txt',
+		'bsml'       => 'bsml',
+		'bsml_sax'   => 'bsml',
+		'chadoxml'   => 'xml',
+		'chaos'      => 'chaos',
+		'chaosxml'   => 'xml',
+		'ctf'        => 'ctf',
+		'embl'       => 'emb',
+		'entrezgene' => 'asn1',
+		'excel'      => 'xls',
+		'exp'        => 'exp',
+		'fasta'      => 'fa',
+		'fastq'      => 'fastq',
+		'game'       => 'xml',
+		'gcg'        => 'gcg',
+		'genbank'    => 'gbk',
+		'interpro'   => 'xml',
+		'kegg'       => 'kegg',
+		'largefasta' => 'lfa',
+		'lasergene'  => 'lasergene',
+		'locuslink'  => 'll_tmpl',
+		'phd'        => 'phred',
+		'pir'        => 'pir',
+		'pln'        => 'pln',
+		'qual'       => 'phred',
+		'raw'        => 'txt',
+		'scf'        => 'scf',
+		'seqxml'     => 'xml',
+		'strider'    => 'strider',
+		'swiss'      => 'sp',
+		'tab'        => 'tsv',
+		'tigr'       => 'xml',
+		'tigrxml'    => 'xml',
+		'tinyseq'    => 'xml',
+		'ztr'        => 'ztr',
+	);
+
+	if($suffix_map{lc($self->format())}){
+		return $suffix_map{lc($self->format())};
+	}else{
+		return 'unknown';
+	}
+}
+
+no Moose;
+1;
+
+__END__
+
+=pod
+
+=encoding UTF-8
+
+=head1 NAME
+
+CPT::Writer::Genomic
+
+=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