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Hi Pengfei,<br>
<br>
I am not entirely sure which data you are looking at, but depending
on the databases, not all genes will have a description or an
external_name.<br>
<br>
For a given gene, we assign a display xref if we find an external
reference from a trusted source matching the ensembl gene.<br>
That xref (external reference) is then used to assign a display name
to the gene.<br>
If there is no such external reference, the gene will have no
display name and we will use the ensembl stable id instead.<br>
<br>
A similar rule applies to assigning descriptions.<br>
<br>
<br>
Hope that helps,<br>
Magali<br>
<br>
<div class="moz-cite-prefix">On 10/02/2014 05:22, 刘鹏飞 wrote:<br>
</div>
<blockquote
cite="mid:CAH_jMvv+z1G21GfqObhLsTdpuqEvGgEUjx-PnNBwY7w1W0Y6Jw@mail.gmail.com"
type="cite">
<div dir="ltr">
<div>Hi Magali and <br>
</div>
<div>Hi all,<br>
<br>
</div>
<div>I use following code to fetch all information of genes for
a bacteria, but get some errors (althouth I could get all data
I wanted), but I could not figure out where goes wrong,
thanks:<br>
</div>
<div>errors:<br>
Use of uninitialized value in print at HZ254_genedata.pl line
20.<br>
<br>
scripts:<br>
# methanocella_conradii_hz254 <br>
#HZ254_genedata.pl<br>
#!/usr/bin/perl<br>
use strict;<br>
use warnings;<br>
use Bio::EnsEMBL::LookUp;<br>
# load the lookup from the main Ensembl Bacteria public server<br>
my $lookup = Bio::EnsEMBL::LookUp->new(<br>
-URL => "<a moz-do-not-send="true"
href="http://bacteria.ensembl.org/registry.json">http://bacteria.ensembl.org/registry.json</a>",<br>
-NO_CACHE => 1<br>
);<br>
# find the correct database adaptor using a unique name<br>
my ($dba) = @{$lookup->get_by_name_exact(<br>
'methanocella_conradii_hz254'<br>
)};<br>
my $genes = $dba->get_GeneAdaptor()->fetch_all(); <br>
# get all gene infomation<br>
open (MYFILE, '>>HZ254gene_data.txt');<br>
foreach my $gene (@$genes){<br>
print $gene->stable_id,"\t", <br>
$gene->display_id,"\t",<br>
$gene->description,"\t", <br>
$gene->start, " - ", <br>
$gene->end, "\t", <br>
$gene->external_name, "\t",<br>
$gene->length,"\n";<br>
};<br>
close (MYFILE);<br>
</div>
<div>##API version 74<br>
<br>
</div>
<div>
<div>
<div><br>
-- <br>
<div>Pengfei Liu, PhD Candidate<br>
<br>
Lab of Microbial Ecology<br>
College of Resources and Environmental Sciences<br>
China Agricultural University<br>
No.2 Yuanmingyuanxilu, Beijing, 100193<br>
P.R. China<br>
<br>
Tel: +86-10-62731358<br>
Fax: +86-10-62731016<br>
<br>
E-mail: <a moz-do-not-send="true"
href="mailto:liupfskygre@gmail.com" target="_blank">liupfskygre@gmail.com</a></div>
<div> </div>
<div>If you are afraid of tomorrow, how can you enjoy
today! </div>
<div>Keep hungry, Keep foolish! </div>
<div>Moving forward!</div>
</div>
</div>
</div>
</div>
</blockquote>
<br>
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