[DAS] Small bug in LDAS

[Lincoln Stein]

Gee, thanks!

Lincoln

Leonardo Marino-Ramirez writes:
 > 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
 > ___ _/      _/     _/ ________________________________________________
 > 
 > 
 > 
 > 
 > _______________________________________________
 > DAS mailing list
 > DAS@biodas.org
 > http://biodas.org/mailman/listinfo/das

-- 
========================================================================
Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org			                  Cold Spring Harbor, NY
Positions available at my lab: see http://stein.cshl.org/#hire
========================================================================