--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cpt_psm_plotter/lib/CPT/Bio/DataSource/Chado.pm	Tue Jul 05 05:40:36 2022 +0000
@@ -0,0 +1,125 @@
+package CPT::Bio::DataSource::Chado;
+no warnings;
+use Moose;
+with 'CPT::Bio::DataSource';
+
+has 'host' => ( is => 'rw', isa => 'Str' );
+has 'pass' => ( is => 'rw', isa => 'Str' );
+has 'user' => ( is => 'rw', isa => 'Str' );
+has 'name' => ( is => 'rw', isa => 'Str' );
+has 'port' => ( is => 'rw', isa => 'Str' );
+
+has 'landmark' => ( is => 'rw', isa => 'Str' );
+has 'organism' => ( is => 'rw', isa => 'Str' );
+
+
+sub getSeqIO {
+	my ($self) = @_;
+	require CPT::Chado::GMOD_Conf;
+
+	my $db = Bio::DB::Das::Chado->new(
+		-dsn      => sprintf( 'dbi:Pg:dbname=%s;host=%s;port=%s', $self->name(), $self->host(), $self->port() ),
+		-user     => $self->user(),
+		-pass     => $self->pass(),
+		-organism => $self->organism(),
+		-inferCDS => 1,
+
+	);
+
+	# Get a list of "segments". Essentially (seqlen IS NOT NULL)
+	my @segments = $db->segment( -name => $self->{'landmark'} );
+
+	# TODO: Need to have a fallback method
+	# Should only produce ONE since we specify landmark exactly
+	foreach my $segment (@segments) {
+		my $stream = $segment->get_feature_stream();
+		use Bio::Seq;
+		my $seq_obj = Bio::Seq->new(
+			-seq        => $segment->seq->seq(),
+			-display_id => $segment->id()
+		);
+		use Bio::SeqFeature::Generic;
+		while ( my $feat = $stream->next_seq ) {
+
+			# In an IDEAL world we'd just do $seq_obj->add_SeqFeature($feat);
+			#
+			# HOWEVER.
+			#
+			# ------------- EXCEPTION: Bio::Root::NotImplemented -------------
+			# MSG: Abstract method "Bio::DB::Das::Chado::Segment::Feature::attach_seq" is not implemented by package Bio::DB::Das::Chado::Segment::Feature.
+			# This is not your fault - author of Bio::DB::Das::Chado::Segment::Feature should be blamed!
+			# STACK: Error::throw
+			# STACK: Bio::Root::Root::throw /usr/local/share/perl/5.14.2/Bio/Root/Root.pm:472
+			# STACK: Bio::Root::RootI::throw_not_implemented /usr/local/share/perl/5.14.2/Bio/Root/RootI.pm:748
+			# STACK: Bio::DB::Das::Chado::Segment::Feature::attach_seq /usr/local/share/perl/5.14.2/Bio/DB/Das/Chado/Segment/Feature.pm:374
+			# STACK: Bio::Seq::add_SeqFeature /usr/local/share/perl/5.14.2/Bio/Seq.pm:1148
+			# STACK: chado_export.pl:59
+			# ----------------------------------------------------------------
+
+			# BUT WE CAN'T. >_>  rageface.tiff
+
+			my %keys;
+			foreach my $tag ( $feat->get_all_tags() ) {
+				my @values = $feat->get_tag_values($tag);
+				if ( $tag eq 'Note' ) {
+					$tag = 'note';
+				}
+				if ( $tag eq 'Dbxref' ) {
+					$tag = 'db_xref';
+
+					#@values = map { if($_ ne 'GFF_source:Genbank'){ $_ } } @values;
+					@values = grep !/GFF_source:Genbank/, @values;
+				}
+				$keys{$tag} = \@values;
+			}
+
+			#print $feat->gff_string(),"\n";
+			my $new_feat = new Bio::SeqFeature::Generic(
+				-start       => $feat->start(),
+				-end         => $feat->end(),
+				-strand      => $feat->strand(),
+				-primary_tag => $feat->primary_tag(),
+				-tag         => \%keys,
+			);
+			$seq_obj->add_SeqFeature($new_feat);
+		}
+
+		return $seq_obj;
+	}
+
+}
+
+no Moose;
+1;
+
+__END__
+
+=pod
+
+=encoding UTF-8
+
+=head1 NAME
+
+CPT::Bio::DataSource::Chado
+
+=head1 VERSION
+
+version 1.99.4
+
+=head2 getSeqIO
+
+supposed to get a seqIO object from a chado DB. not fully implemented
+
+=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