From 624acfd0ac430393505f995a2ab08bdeb40bf71b Mon Sep 17 00:00:00 2001
From: daisie_local <daisieh@gmail.com>
Date: Wed, 18 Mar 2015 13:53:50 -0700
Subject: [PATCH] simplify_genbank_array

---
 lib/Genbank.pm      | 23 +++++++++++++++++++++--
 lib/Subfunctions.pm |  2 +-
 parsing/genbank.pl  |  3 ++-
 3 files changed, 24 insertions(+), 4 deletions(-)

diff --git a/lib/Genbank.pm b/lib/Genbank.pm
index b802134..45f38dd 100755
--- a/lib/Genbank.pm
+++ b/lib/Genbank.pm
@@ -18,7 +18,7 @@ BEGIN {
 	# Inherit from Exporter to export functions and variables
 	our @ISA         = qw(Exporter);
 	# Functions and variables which are exported by default
-	our @EXPORT      = qw(parse_genbank sequence_for_interval sequin_feature stringify_feature parse_feature_desc parse_interval parse_qualifiers within_interval write_sequin_tbl feature_table_from_genbank set_sequence get_sequence get_name write_features_as_fasta clone_features);
+	our @EXPORT      = qw(parse_genbank sequence_for_interval sequin_feature stringify_feature parse_feature_desc parse_interval parse_qualifiers within_interval write_sequin_tbl feature_table_from_genbank set_sequence get_sequence get_name write_features_as_fasta clone_features simplify_genbank_array);
 	# Functions and variables which can be optionally exported
 	our @EXPORT_OK   = qw();
 }
@@ -99,6 +99,25 @@ sub parse_genbank {
 	return \@gene_array;
 }
 
+sub simplify_genbank_array {
+	my $gene_array = shift;
+
+	my @simplified_array = ();
+	foreach my $feat (@$gene_array) {
+		if ($feat->{'type'} =~ /gene|source/) {
+			my @newcontains = ();
+			foreach my $subfeat (@{$feat->{'contains'}}) {
+				if ($subfeat->{'type'} !~ /exon|intron|STS/) {
+					push @newcontains, $subfeat;
+				}
+			}
+			$feat->{'contains'} = \@newcontains;
+			push @simplified_array, $feat;
+		}
+	}
+	return \@simplified_array;
+}
+
 sub parse_feature_sequences {
 	my $gene_array = shift;
 
@@ -244,7 +263,7 @@ sub write_sequin_tbl {
 
 sub feature_table_from_genbank {
 	my $gbfile = shift;
-	my $gene_array = Genbank::parse_genbank($gbfile);
+	my $gene_array = Genbank::simplify_genbank_array(Genbank::parse_genbank($gbfile));
 
 	my @feature_array = ();
 	foreach my $gene (@$gene_array) {
diff --git a/lib/Subfunctions.pm b/lib/Subfunctions.pm
index 1272f7f..0b49660 100644
--- a/lib/Subfunctions.pm
+++ b/lib/Subfunctions.pm
@@ -1144,7 +1144,7 @@ sub blast_to_genbank {
 	my $gbfile = shift;
 	my $fastafile = shift;
 
-	my $gene_array = Genbank::parse_genbank($gbfile);
+	my $gene_array = Genbank::simplify_genbank_array(Genbank::parse_genbank($gbfile));
 	my $refseq = Genbank::get_sequence();
 	my ($ref_hash, $region_array) = Genbank::clone_features($gene_array);
 	my ($query_hash, $query_array) = parse_fasta($fastafile);
diff --git a/parsing/genbank.pl b/parsing/genbank.pl
index 16ed441..cec80f6 100755
--- a/parsing/genbank.pl
+++ b/parsing/genbank.pl
@@ -18,7 +18,8 @@
 	$outfile = $gbfile;
 }
 
-my $gene_array = Genbank::parse_genbank($gbfile);
+my $gene_array = Genbank::simplify_genbank_array(Genbank::parse_genbank($gbfile));
+
 
 open FASTA_FH, ">", "$outfile.fasta";
 print FASTA_FH Genbank::write_features_as_fasta ($gene_array);