From b28cef3987873b717019881eae413bd03651c9ee Mon Sep 17 00:00:00 2001
From: Brian Osborne <briano@bioteam.net>
Date: Tue, 29 Jan 2013 08:33:49 -0500
Subject: [PATCH] In progress

---
 lib/diya/BDRD/rpsblastCDS.pm | 14 +++++------
 scripts/extractCDS.pl        | 48 ++++++++++++++++++++++--------------
 2 files changed, 37 insertions(+), 25 deletions(-)

diff --git a/lib/diya/BDRD/rpsblastCDS.pm b/lib/diya/BDRD/rpsblastCDS.pm
index b77d5c7..e35cfab 100644
--- a/lib/diya/BDRD/rpsblastCDS.pm
+++ b/lib/diya/BDRD/rpsblastCDS.pm
@@ -109,15 +109,15 @@ sub parse {
 
         if ( $feat->primary_tag eq 'CDS' ) {
 
-            my @locus = $feat->get_tag_values('locus_tag');
+            my ($locus) = $feat->get_tag_values('locus_tag');
 
             my $fh;
 
-            eval { $fh = $index->get_stream( $locus[0] ); };
+            eval { $fh = $index->get_stream( $locus ); };
 
             if ($@) {
                 print "Problem retrieving "
-                  . $locus[0]
+                  . $locus
                   . " from $blastout.index\n";
                 next;
             }
@@ -141,7 +141,7 @@ sub parse {
 
                 print "Found rpsblast hit "
                   . $hit->description
-                  . " for $locus[0]\n"
+                  . " for $locus\n"
                   if $diya->verbose;
 
                 # get domain id from hit
@@ -166,11 +166,11 @@ sub parse {
 
                 }
 
-                my @products = $feat->get_tag_values('product')
+                my ($product) = $feat->get_tag_values('product')
                   if ( $feat->has_tag('product') );
 
                 # If this feature is already annotated with a UniRef match
-                if ( $products[0] =~ /RepID=/ && defined $tags->{'product'} ) {
+                if ( $product =~ /RepID=/ && defined $tags->{'product'} ) {
 
                     my $note = "similar to " . $tags->{'product'};
                     $note .= " " . $tags->{'cluster'};
@@ -332,7 +332,7 @@ sub load_cdd_table {
             $cddmap{$id} = \%cluster;
         }
 
-# 103623 PRK08948 PRK08948 2-octaprenyl-6-methoxyphenyl hydroxylase; Validated	392
+# 103623	PRK08948	PRK08948	2-octaprenyl-6-methoxyphenyl hydroxylase; Validated	392
         if ( $line =~ /^\d+\s+(PRK\d+)\s+\w+\s+([^;]+)/ ) {
             my ( $id, $def ) = ( $1, $2 );
             $def =~ s/\s+$//;
diff --git a/scripts/extractCDS.pl b/scripts/extractCDS.pl
index 47dec73..81ff275 100755
--- a/scripts/extractCDS.pl
+++ b/scripts/extractCDS.pl
@@ -7,7 +7,7 @@ =head1 NAME
 =head1 DESCRIPTION
 
 Extracts the CDS features from a GenBank file and creates nucleotide and
-peptide fasta files containing all genes and translations.
+peptide fasta files containing them.
 
      gene            complement(32855..33520)
                      /locus_tag="test0001_380"
@@ -23,32 +23,44 @@ =head1 DESCRIPTION
 use Bio::Seq;
 use Data::Dumper;
 
-my ($inputfile,$outputfile) = @ARGV;
+my ( $inputfile, $outputfile ) = @ARGV;
 
-die "Need both input file name and output file name" 
+die "Need both input file name and output file name"
   unless ( $inputfile && $outputfile );
 
-my $in = Bio::SeqIO->new( -file => "$inputfile.gbk",
-			  -format => 'genbank' );
+my $in = Bio::SeqIO->new(
+    -file   => "$inputfile.gbk",
+    -format => 'genbank'
+);
 
-my $ntout = Bio::SeqIO->new( -file => ">>$outputfile",
-			   -format => 'fasta' );
+my $out = Bio::SeqIO->new(
+    -file   => ">>$outputfile",
+    -format => 'fasta'
+);
 
-my $pepout = Bio::SeqIO->new( -file => ">>$outputfile.pep",
-			      -format => 'fasta' );
+my $pepout = Bio::SeqIO->new(
+    -file   => ">>$outputfile.pep",
+    -format => 'fasta'
+);
 
 my $gbk = $in->next_seq;
 
 for my $feature ( $gbk->get_SeqFeatures ) {
     if ( $feature->primary_tag eq "gene" ) {
-		my @ids = $feature->get_tag_values("locus_tag");
-		my $str = $feature->seq->seq;
-		my $seq = Bio::Seq->new( -seq => $str,
-								 -display_id => "@ids" );
-		$ntout->write_seq($seq);
-
-		$seq = $seq->revcom if ( $feature->location->start > $feature->location->end );
-		my $pep = $seq->translate(-complete => 1);
-		$pepout->write_seq($pep);
+        my @ids = $feature->get_tag_values("locus_tag");
+        my $str = $feature->seq->seq;
+        my $seq = Bio::Seq->new(
+            -seq        => $str,
+            -display_id => "@ids"
+        );
+        $out->write_seq($seq);
+
+        $seq = $seq->revcom
+          if ( $feature->location->start > $feature->location->end );
+        my $pep = $seq->translate( -complete => 1 );
+        $pepout->write_seq($pep);
     }
 }
+
+__END__
+