[Bioperl-l] Download sequence by genomic location

[Peng Yu]

I didn't see a document for Bio::Das in my bioperl,

$ perldoc Bio::Das
No documentation found for "Bio::Das".
$ perldoc Bio::Das::SegmentI
$ perldoc Bio::Das::FeatureTypeI

I thought that maybe my bioperl installation is corrupted. Then I
install Bio::Das (cpan Bio::Das), which was unsuccessful. Then I
install it by "cpan -f Bio::Das".

I also manually installed IO-Socket-SSL-1.33.tar.gz. Then try the
example. It seems that the there is still something missing. I guess
there must be some problem with my bioperl installation.

Shall I reinstall it? Is there an easy fix?

$ ./main.pl
Using password in unencrypted URI against RFC #2396 recommendation at
/home/pengy/utility/linux/opt/perl-5.10.1/lib/site_perl/5.10.1/Bio/Das/HTTP/Fetch.pm
line 331.
Must have IO::Socket::SSL installed to use https: urls: Can't locate
Net/SSLeay.pm in @INC (@INC contains:
/home/pengy/utility/linux/opt/perl-5.10.1/lib/5.10.1/x86_64-linux
/home/pengy/utility/linux/opt/perl-5.10.1/lib/5.10.1
/home/pengy/utility/linux/opt/perl-5.10.1/lib/site_perl/5.10.1/x86_64-linux
/home/pengy/utility/linux/opt/perl-5.10.1/lib/site_perl/5.10.1 .) at
/home/pengy/utility/linux/opt/perl-5.10.1/lib/site_perl/5.10.1/IO/Socket/SSL.pm
line 18.
BEGIN failed--compilation aborted at
/home/pengy/utility/linux/opt/perl-5.10.1/lib/site_perl/5.10.1/IO/Socket/SSL.pm
line 18.
Compilation failed in require at (eval 41) line 3.
 at /home/pengy/utility/linux/opt/perl-5.10.1/lib/site_perl/5.10.1/Bio/Das.pm
line 200

$ cat main.pl
#!/usr/bin/env perl

use strict;
use warnings;
use Bio::Das;

my $das = Bio::Das->new(5);  # timeout of 5 sec
my @response = $das->dsn('http://stein.cshl.org/perl/das',
  'http://genome.cse.ucsc.edu/cgi-bin/das',
  'http://user:pass@www.wormbase.org/db/das',
  'https://euclid.well.ox.ac.uk/cgi-bin/das',
);

for my $url (@response) {
  if ($url->is_success) {
    my @dsns = $url->results;
    print "$url:\t\n";
    foreach (@dsns) {
      print "\t",$_->url,"\t",$_->description,"\n";
    }
  } else {
    print "$url: ",$url->error,"\n";
  }
}


On Wed, Jul 28, 2010 at 5:47 PM, Chris Fields <cjfields at illinois.edu> wrote:
> Forgot completely, but this should be possible via Bio::DAS:
>
> http://search.cpan.org/~lds/Bio-Das-1.06/Das.pm
>
> I have used it myself via GBrowse.
>
> chris
>
> On Jul 28, 2010, at 5:14 PM, Peng Yu wrote:
>
>> I could download a sequence by location at genome browser.
>>
>> http://genome.ucsc.edu/cgi-bin/hgc?hgsid=166347358&o=38129163&g=getDna&i=mixed&c=chr13&l=38129163&r=38153298&db=mm9&hgsid=166347358
>>
>> I know that there are ways to get the sequence. But I don't see a way
>> to get the sequence by location. Could anybody let me know if there is
>> such a function in bioperl?
>> http://www.bioperl.org/wiki/HOWTO:Beginners#Retrieving_a_sequence_from_a_database
>>
>> --
>> Regards,
>> Peng
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>



-- 
Regards,
Peng