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Hi,<br>
I am using the code from the API installation page and that page
talks about version 64.<br>
<a class="moz-txt-link-freetext" href="http://www.ensembl.org/info/docs/api/api_installation.html">http://www.ensembl.org/info/docs/api/api_installation.html</a><br>
<br>
This is my output under verbose, looks like it is connecting.<br>
Odd number of elements in hash assignment at
/usr/mbu/software/ensembl/ensembl/modules/Bio/EnsEMBL/Utils/Argument.pm
line 148.<br>
Transcript:ENSDART00000112153 Gene:ENSDARG00000090113 Chr:19
Start:33519855 End:33522332<br>
Can't call method "get_all_Member_Attribute" on an undefined value
at sandbox3.pl line 47.<br>
<br>
Regards,<br>
James<br>
<br>
<br>
On 11/11/2011 20:20, Javier Herrero wrote:
<blockquote cite="mid:4EBD83A4.6010406@ebi.ac.uk" type="cite">
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
Hi James<br>
<br>
This error is typical when you fail to connect to the database.<br>
<br>
I suspect you are using the HEAD code instead of the branch 64.
The head code is already configured for connecting to the
forthcoming database. Please switch your code to the 64 branch and
try again:<br>
<br>
cvs up -r branch-ensembl-64<br>
<br>
Regards<br>
<br>
Javier<br>
<br>
On 11/11/11 19:29, Jan Vogel wrote:
<blockquote
cite="mid:E9D90243-F58A-4D04-B289-171286BEBF4B@gmail.com"
type="cite"><span class="Apple-tab-span" style="white-space:pre">
</span>
<div><span class="Apple-tab-span" style="white-space:pre"><span
class="Apple-style-span" style="white-space: normal; ">Hi
James, </span>
<div style="white-space: normal; "><br>
</div>
<div style="white-space: normal; ">the first script from the
powerpoint works for me w/o problems or modifications.
I've tried schema 62 and schema 64 API's. </div>
<div style="white-space: normal; "><br>
</div>
<div style="white-space: normal; "><br>
</div>
<div style="white-space: normal; ">The second one ( 'from
the list' ) had some minor problems. It works like this : </div>
<div style="white-space: normal; "><br>
</div>
<div style="white-space: normal; "><font
class="Apple-style-span" face="Courier">my $member =
$member_adaptor->fetch_by_source_stable_id('ENSEMBLGENE','ENSG00000004059');</font></div>
<div style="white-space: normal; "><font
class="Apple-style-span" face="Courier"><br>
</font></div>
<div style="white-space: normal; "><font
class="Apple-style-span" face="Courier">or </font></div>
<div style="white-space: normal; "><font
class="Apple-style-span" face="Courier"><br>
</font></div>
<div style="white-space: normal; "><font
class="Apple-style-span" face="Courier">
<div style="font-family: Helvetica; "><font
class="Apple-style-span" face="Courier">my $member =
$member_adaptor->fetch_by_source_stable_id(undef,'ENSG00000004059');</font></div>
<div><font class="Apple-style-span" face="Helvetica"><font
class="Apple-style-span" face="Courier"><br>
</font></font></div>
<div><font class="Apple-style-span" face="Helvetica"><font
class="Apple-style-span" face="Courier">I did not
try the zfish protein. </font></font></div>
<div><font class="Apple-style-span" face="Helvetica"><font
class="Apple-style-span" face="Courier"><br>
</font></font></div>
<div>Hth, </div>
<div> Jan </div>
</font></div>
<div style="white-space: normal; ">
<div><br>
</div>
<div>
<div>On Nov 11, 2011, at 9:50 AM, James Blackshaw wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div>Hi,<br>
I've been trying to put together some scripts for
finding the homolgies<br>
for some lists of genes I'm interested in, but I
keep getting errors<br>
with the "fetch" methods.<br>
<br>
"Can't call method "fetch_by_source_stable_id" on an
undefined value at<br>
<a moz-do-not-send="true" href="http://sandbox3.pl/">sandbox3.pl</a> line
15."<br>
<br>
I've used one script taken from a presentation by
Stephen Fitzgerald at<br>
Edinburgh, and another from this maining list. I'm
including both.<br>
<br>
From the powerpoint:<br>
use strict;<br>
use Bio::EnsEMBL::Registry;<br>
my $reg = "Bio::EnsEMBL::Registry";<br>
<br>
$reg->load_registry_from_db(<br>
-host=>"<a moz-do-not-send="true"
href="http://ensembldb.ensembl.org/">ensembldb.ensembl.org</a>",<br>
-user => "anonymous");<br>
<br>
<br>
my $ma = $reg->get_adaptor(<br>
"Multi", "compara", "Member");<br>
my $member = $ma->fetch_by_source_stable_id(<br>
"ENSEMBLGENE", "ENSG00000000971");<br>
<br>
my $homology_adaptor = $reg->get_adaptor(<br>
"Multi", "compara", "Homology");<br>
<br>
my $homologies = $homology_adaptor-><br>
fetch_all_by_Member($member);<br>
<br>
foreach my $this_homology (@$homologies) {<br>
print $this_homology->description, "\n";<br>
my $member_attributes = $this_homology-><br>
get_all_Member_Attribute();<br>
foreach my $this_mem_attr (@$member_attributes) {<br>
my ($this_member, $this_attribute) =<br>
@$this_mem_attr;<br>
print $this_member->genome_db->name, " ",<br>
$this_member->source_name, " ",<br>
$this_member->stable_id, "\n";<br>
}<br>
print "\n";<br>
}<br>
<br>
==========================================<br>
<br>
From the list:<br>
use Bio::EnsEMBL::Registry;<br>
Bio::EnsEMBL::Registry->load_registry_from_db(<br>
-host => 'ensembldb.ensembl.org',<br>
-user => 'anonymous',<br>
-port => 5306);<br>
my $member_adaptor =
Bio::EnsEMBL::Registry->get_adaptor(<br>
'Multi','compara','Member');<br>
<br>
# fetch a Member<br>
# get the MemberAdaptor<br>
my $member_adaptor =<br>
Bio::EnsEMBL::Registry->get_adaptor('Multi','compara','Member');<br>
<br>
# fetch a Memmy $member =<br>
$member_adaptor->fetch_by_source_stable_id('ENSEMBLPROTEIN','ENSG00000004059');<br>
my $member =<br>
$member_adaptor->fetch_by_source_stable_id('ENSEMBLPEP','ENSDARP00000103634');<br>
# print out some information about the Member<br>
print $member->description, "\n";<br>
<br>
<br>
<br>
my $homology_adaptor =
Bio::EnsEMBL::Registry->get_adaptor('Multi',<br>
'compara', 'Homology');<br>
my $homologies =
$homology_adaptor->fetch_all_by_Member($member);<br>
<br>
# That will return a reference to an array with all<br>
homologies(orthologues in<br>
# other species and paralogues in the same one)<br>
# Then for each homology, you can get all the
Members implicated<br>
<br>
foreach my $homology (@{$homologies}) {<br>
# You will find different kind of description<br>
# UBRH, MBRH, RHS, YoungParalogues<br>
# see ensembl-compara/docs/docs/schema_doc.html for
more details<br>
<br>
print $homology->description," ",
$homology->subtype,"\n";<br>
# And if they are defined dN and dS related values<br>
print " dn ", $homology->dn,"\n";<br>
print " ds ", $homology->ds,"\n";<br>
print " dnds_ratio ",
$homology->dnds_ratio,"\n";<br>
}<br>
<br>
my $homology = $homologies->[0];<br>
# take one of the homologies and lookinto it<br>
<br>
foreach my $member_attribute
(@{$homology->get_all_Member_Attribute}) {<br>
<br>
# for each Member, you get information on the
Member specifically and in<br>
# relation to the homology relation via Attribute
object<br>
<br>
my ($member, $attribute) = @{$member_attribute};<br>
print (join " ", map { $member->$_ }
qw(stable_id taxon_id))."\n";<br>
print (join " ", map { $attribute->$_ }
qw(perc_id<br>
perc_posperc_cov))."\n";<br>
<br>
}<br>
====================================================<br>
<br>
<br>
<br>
James Blackshaw<br>
PhD Student<br>
MRC Mitochondrial Biology Unit<br>
<br>
<br>
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Ensembl Blog: <a moz-do-not-send="true"
href="http://www.ensembl.info/">http://www.ensembl.info/</a><br>
</div>
</blockquote>
</div>
<div><br>
</div>
</div>
</span></div>
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<pre wrap="">_______________________________________________
Dev mailing list <a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:Dev@ensembl.org">Dev@ensembl.org</a>
List admin (including subscribe/unsubscribe): <a moz-do-not-send="true" class="moz-txt-link-freetext" href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a>
Ensembl Blog: <a moz-do-not-send="true" class="moz-txt-link-freetext" href="http://www.ensembl.info/">http://www.ensembl.info/</a>
</pre>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Javier Herrero, PhD
Ensembl Compara Project Leader
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge - CB10 1SD - UK</pre>
<br>
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List admin (including subscribe/unsubscribe): <a class="moz-txt-link-freetext" href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a>
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</pre>
</blockquote>
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