[ensembl-dev] Cannot get sequence from genome using perl variables (no HTML)

[Damian]

Hi Bert,
Thanks for the quick reply.
I have tried it without the quotes around the '1' and it does work.
So:

$chr = 1;
$start = 724572;
$end = 724726;
$slice = $slice_adaptor->fetch_by_region( 'chromosome', $chr, $start, $end );
$x = $slice->seq;

Will work.


However this code doesn't work:

$coords = "1,724572,724726";
@ary = split(/,/, $coords);
$chr = $ary[0];
$e_start = $ary[1];
$e_end = $ary[2];

## get the sequence coordinates.
print STDERR "$coords\n";
print STDERR "|$chr|\n";
print STDERR "|$e_start|\n";
print STDERR "|$e_end|\n";

$slice = $slice_adpator->fetch_by_region( 'chromosome', $chr, $e_start, 
$e_end );
$x = $slice->seq;
print "\n$x\n";

And throws the error:
Can't call method "fetch_by_region" on an undefined value at genSeqs.pl 
line 39.

Any ideas?

Damian



On 04/27/2011 11:48 AM, Bert Overduin wrote:
> Hi Damian,
>
> Haven't you put a few too many quotation marks around the 1?
>
> Cheers,
> Bert
>
> Sent from my iPhone
>
> On Apr 27, 2011, at 4:41 PM, Damian<dfermin at umich.edu>  wrote:
>
>> Hello.
>>
>> Sorry for double posting. My message go corrupted since I sent it via HTML..
>>
>> Down below I've pasted a snippet of a script I've written to retrieve regions of the genome.
>> The first call to slice_adaptor works as expected. This call uses the hard coded coordinates.
>> The second version of the call to slice_adaptor fails to work, throwing the error:
>> Can't call method "seq" on an undefined value at getSeqs.pl line 23.
>>
>> The only difference between the two calls to slice_adaptor is that the second version uses perl variables ($chr, $start, $end) instead of the hard coded values.
>> Is this a bug or am I doing something wrong?
>> I'm using Ensembl Perl API version 62 with the Human database installed (homo_sapiens_core_62_37g).
>>
>> Thanks in advance for any and all help.
>> Damian
>>
>>
>> #!/usr/bin/perl -w
>>
>> use Bio::EnsEMBL::Registry;
>> use Bio::EnsEMBL::Slice;
>>
>> my $registry = 'Bio::EnsEMBL::Registry';
>> $registry->load_registry_from_db(
>>     -host =>  '127.0.0.1',
>>     -user =>  'jonDoe'
>> );
>>
>> $slice_adaptor = $registry->get_adaptor('Human', 'Core', 'Slice');
>>
>> $slice = $slice_adaptor->fetch_by_region( 'chromosome', '1', 724572, 724726 );
>> $x = $slice->seq;
>> print "\n## 1 ###\n$x\n\n";
>>
>> ## this version does NOT work
>> $chr = "'1'";
>> $start = 724572;
>> $end = 724726;
>> $slice = $slice_adaptor->fetch_by_region( 'chromosome', $chr, $start, $end );
>> $x = $slice->seq;
>> print "\n## 2 ###\n$x\n\n";
>>
>> exit;
>>
>> -- 
>> ------------------------------------------------------------------------------
>> Damian Fermin, Ph.D.
>> Pathology Department
>> University of Michigan
>> 4237 Medical Science I
>> 1301 Catherine
>> Ann Arbor, MI 48109-0602
>> 734.615.0302
>>
>> "There is No Gene for the Human Spirit"
>>     -- GATTACA
>> ------------------------------------------------------------------------------
>>
>>
>> _______________________________________________
>> Dev mailing list    Dev at ensembl.org
>> List admin (including subscribe/unsubscribe): http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog: http://www.ensembl.info/
>

-- 
------------------------------------------------------------------------------
Damian Fermin, Ph.D.
Pathology Department
University of Michigan
4237 Medical Science I
1301 Catherine
Ann Arbor, MI 48109-0602
734.615.0302

"There is No Gene for the Human Spirit"
	-- GATTACA
------------------------------------------------------------------------------