SynTView project is hosted on a Redmine Server : SynTView (see Guide) with a svn repository
Copyright (C) 2011 Institut PASTEUR
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version



Please visit Tango(Toolkit for ANalysis nGs Outputs) web site to obtain script to compute SNPs calling.

			#!/usr/bin/perl -w
use strict;
use Bio::SeqIO;

my $gbk = Bio::SeqIO->new(-fh=>\*STDIN, -format=>'genbank');
my $seq = $gbk->next_seq;
my @cds = grep { $_->primary_tag eq 'CDS' } $seq->get_SeqFeatures;

print $seq->description, " - 0..",$seq->length,"\n";
print scalar(@cds)," proteins\n";
print join("\t", qw(Location Strand Length PID Gene Synonym Code COG 
Product)),"\n";

for my $f (@cds) {
   my $gi = '-';
   $gi = $1 if tag($f, 'db_xref') =~ m/\bGI:(\d+)\b/;
   my $cog = '-';
   $cog = $1 if tag($f, 'product') =~ m/^(COG\S+)/;
   my @col = (
     $f->start.'..'.$f->end,
     $f->strand >= 0 ? '+' : '-',
     ($f->length/3)-1,
     '-',
     $gi,
     tag($f, 'locus_tag'),
     tag($f, 'gene'),
     $cog,
     tag($f, 'product'),
   );
   print join("\t", @col), "\n";
}

sub tag {
   my($f, $tag) = @_;
   return '-' unless $f->has_tag($tag);
   return join(' ', $f->get_tag_values($tag));
}