[DAS] Small bug in LDAS

[Leonardo Marino-Ramirez]

Dear all,

I am testing the LDAS server to provide annotations from a database
created with GMOD and I found a small bug in the das script:

I was trying to interface with the Bio::DAS library and I was getting no
dna output from the script below:

#!/usr/local/bin/perl
#
# PROGRAM  : das_tofu
#
# PURPOSE  : Simple driver for Bio::Das get features associated with
#            a genomic region
#

use strict;
use Bio::Das;
use Getopt::Std;

use vars qw($opt_d
            $opt_s
            $opt_e
            );

getopt('dse');

# contact a DAS server using the "ecoli" data source
my $das      = Bio::Das->new('http://tofu.tamu.edu/cgi-bin/das' =>
$opt_d);

# fetch a segment
my $segment  = $das->segment(-ref=>'K12',-start=>$opt_s,-stop=>$opt_e);

# get features and DNA from segment
my @features = $segment->features;
my $dna      = $segment->dna;

# find out what data sources are available:
my $db       = Bio::Das->new('http://tofu.tamu.edu/cgi-bin/das');
my @sources  = $db->sources;

# find out what feature types are available
my @types       = $db->types;

# get the entry points
my @entry_poitns = $db->entry_points;

print "Features: @features\n";
print "DNA: $dna\n";
print "Sources: @sources\n";
print "Types: @types\n";
print "Entry points: @entry_poitns\n";

I found that the error was comming from a missing ">". See the diff below:

diff das /home/httpd/cgi-bin/das
1c1
< #!/usr/bin/perl
---
> #!/usr/local/bin/perl
116c116
<   print qq(<?xml version="1.0" standalone="yes"?\n);
---
>   print qq(<?xml version="1.0" standalone="yes"?>\n);

I had to fix the perl path manually also.

Thanks, Leonardo

-- 

___ _/ _______________________________________________________________
   _/
  _/    _/      _/_/_/    Leonardo Marino-Ramirez   lmarino@tamu.edu
 _/    _/_/  _/_/    _/  Biochemistry Department, Texas A&M University
_/_/_/_/  _/  _/_/_/    2128 TAMU, College Station, TX 77843-2128, USA
     _/      _/     _/ Voice: (979) 862-4055   Fax: (979) 845-9274
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