Hello!

I am parsing a Genebank flat file from NCBI (the .gbff.gz found in here). To do this I'm using Bio::SeqIO and I am finding a problem in the very first CDS which looks like this

source          1..4480937
                     /organism="Alteromonas macleodii str. 'Deep ecotype'"
                     /mol_type="genomic DNA"
                     /strain="Deep ecotype"
                     /db_xref="taxon:314275"
gene            join(4480899..4480937,1..1626)
                     /locus_tag="MADE_000001020675"
CDS             join(4480899..4480937,1..1626)
                     /locus_tag="MADE_000001020675"
                     /inference="EXISTENCE: similar to AA
                     sequence:RefSeq:YP_006797084.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="chromosomal replication initiator protein DnaA"
                     /protein_id="AGV54147.1"
                     /db_xref="GI:543176245"
                     /translation="MSLWN...TLSS"

My concern is with this line:

CDS             join(4480899..4480937,1..1626)

However, when I look at the nucleotide sequence that is outputed by Bio::SeqIO, it is outputting ~4.5 million nucleotides whereas if you look at the highlighted area it clearly shows that the coding sequence has ~1600ish nucleotides.What am I doing wrong?

Below you can find a snippet of the code that I am using. The reason why I'm using

next unless (($feat->primary_tag eq "CDS") and $feat->has_tag("translation"));

is that I am only interested in getting protein sequences and their corresponding gene sequences.

Thank you for all help!

#!/usr/local/bin/perl
use strict;
use warnings;
use autodie;
use Data::Dump;
use File::Basename;
use Bio::SeqIO;
use Data::Dumper;

[$gbffpath and other non-relevant stuff hidden]

opendir(DIR, "$gbffpath");
my @files= grep {/\.gbff$/ } readdir(DIR);
closedir(DIR);

my $k=1;
my ($i,$j);
foreach my $f (@files) {
    $i=0;$j=0;
    my $in = Bio::SeqIO -> new( -file => "<$gbffpath\\$f", -format => 'genbank');

    while (my $seq = $in->next_seq) {
        for my $feat ($seq -> get_SeqFeatures) {
            next unless (($feat->primary_tag eq "CDS") and $feat->has_tag("translation"));
            if ($feat->primary_tag eq "CDS") {#use to print DNA

              print $geneout "\>";
              # construct fasta header based on information present for each CDS:
              print $geneout $feat->get_tag_values('locus_tag'),"\|" if ( $feat->has_tag('locus_tag') );    
              print $geneout $feat->get_tag_values('db_xref') ,"\|" if ( $feat->has_tag('db_xref') );    
              print $geneout $feat->get_tag_values('protein_id'),"\|" if ( $feat->has_tag('protein_id') );    
              print $geneout $feat->get_tag_values('gene'),"\|" if ( $feat->has_tag('gene') ); 
              print $geneout $feat->get_tag_values('product'),"\|" if ( $feat->has_tag('product') );
              print $protout $feat->get_tag_values('note'), if ($feat->has_tag('note') );

              # print sequence:
              print $geneout "\n",$feat->seq->seq,"\n";
              $i++;
              }
            }
        }
    }

    if (($i ne $j) or ($i==0) or ($j==0)){
      print "\t\t$f\t$i CDS\t$j prots\t\n" ;
      print "\t\t\>\>\>$f\t$i CDS\t$j prots\t\n";
    }
    else{
      print "Extracted $i\/$j CDS\/proteins from file $f ($k/".($#files+1).")\n";
    }
    $k++;
}