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<font face="Helvetica, Arial, sans-serif">$chr = '1'; instead of </font><font
face="Helvetica, Arial, sans-serif">$chr = "'1'";</font> might
help, I think<br>
<br>
Daniel<br>
<br>
<br>
On 27/04/2011 14:13, Damian wrote:
<blockquote cite="mid:4DB8166E.5020708@umich.edu" type="cite">
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charset=ISO-8859-1">
<font face="Helvetica, Arial, sans-serif">Hello.<br>
<br>
Down below I've pasted a snippet of a script I've written to
retrieve regions of the genome.<br>
The first call to slice_adaptor works as expected. This call
uses the hard coded coordinates.<br>
The second version of the call to slice_adaptor fails to work,
throwing the error: <br>
Can't call method "seq" on an undefined value at getSeqs.pl line
23.<br>
<br>
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.</font><font face="Helvetica,
Arial, sans-serif"><br>
Is this a bug or am I doing something wrong?</font><br>
<font face="Helvetica, Arial, sans-serif">I'm using Ensembl Perl
API version 62 with the Human database installed
(homo_sapiens_core_62_37g).<br>
<br>
Thanks in advance for any and all help.<br>
Damian<br>
<br>
<br>
#!/usr/bin/perl -w<br>
<br>
use Bio::EnsEMBL::Registry;<br>
use Bio::EnsEMBL::Slice;<br>
<br>
my $registry = 'Bio::EnsEMBL::Registry';<br>
$registry->load_registry_from_db(<br>
-host => '127.0.0.1',<br>
-user => 'jonDoe'<br>
);<br>
<br>
$slice_adaptor = $registry->get_adaptor('Human', 'Core',
'Slice');<br>
<br>
$slice = $slice_adaptor->fetch_by_region( 'chromosome', '1',
724572, 724726 );<br>
$x = $slice->seq;<br>
print "\n## 1 ###\n$x\n\n";<br>
<br>
## this version does NOT work<br>
$chr = "'1'";<br>
$start = 724572;<br>
$end = 724726;<br>
$slice = $slice_adaptor->fetch_by_region( 'chromosome', $chr,
$start, $end );<br>
$x = $slice->seq;<br>
print "\n## 2 ###\n$x\n\n";<br>
<br>
exit;<br>
<br>
</font>
<pre class="moz-signature" cols="72">--
------------------------------------------------------------------------------
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
------------------------------------------------------------------------------
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