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Hi Mike,<br>
<br>
Our live mirrors only hold the last two releases.<br>
Giving we are on release 72, you will find 71 and 72 databases
there, but not 70, which is the db_version you specified for your
registry.<br>
<br>
As for the species, if you want to use cat data, you probably want
to replace the human gene_adaptor with a cat one.<br>
<blockquote style="margin: 0 0 0 40px; border: none; padding: 0px;">
<div>
<div>
<div style="word-wrap: break-word; -webkit-nbsp-mode: space;
-webkit-line-break: after-white-space; "><span
style="font-family: Menlo; font-size: 11px; ">L33: </span><span
style="font-family: Menlo; font-size: 11px; color:
rgb(187, 44, 162); ">my </span><span style="font-family:
Menlo; font-size: 11px; ">$human_gene_adaptor =
$reg->get_adaptor(</span><span style="font-family:
Menlo; font-size: 11px; color: rgb(209, 47, 27); ">"Homo
sapiens"</span><span style="font-family: Menlo; font-size:
11px; ">, </span><span style="font-family: Menlo;
font-size: 11px; color: rgb(209, 47, 27); ">"core"</span><span
style="font-family: Menlo; font-size: 11px; ">, </span><span
style="font-family: Menlo; font-size: 11px; color:
rgb(209, 47, 27); ">"Gene"</span><span style="font-family:
Menlo; font-size: 11px; ">);</span></div>
</div>
</div>
</blockquote>
with<br>
<blockquote style="margin: 0 0 0 40px; border: none; padding: 0px;">
<div>
<div>
<div style="word-wrap: break-word; -webkit-nbsp-mode: space;
-webkit-line-break: after-white-space; "><span
style="font-family: Menlo; font-size: 11px; ">L33: </span><span
style="font-family: Menlo; font-size: 11px; color:
rgb(187, 44, 162); ">my </span><span style="font-family:
Menlo; font-size: 11px; ">$cat_gene_adaptor =
$reg->get_adaptor(</span><span style="font-family:
Menlo; font-size: 11px; color: rgb(209, 47, 27); ">"Felis
catus"</span><span style="font-family: Menlo; font-size:
11px; ">, </span><span style="font-family: Menlo;
font-size: 11px; color: rgb(209, 47, 27); ">"core"</span><span
style="font-family: Menlo; font-size: 11px; ">, </span><span
style="font-family: Menlo; font-size: 11px; color:
rgb(209, 47, 27); ">"Gene"</span><span style="font-family:
Menlo; font-size: 11px; ">);<br>
</span></div>
</div>
</div>
</blockquote>
<br>
<br>
Hope that helps,<br>
Magali<br>
<br>
<br>
<div class="moz-cite-prefix">On 29/07/13 23:16, Mike Montague wrote:<br>
</div>
<blockquote
cite="mid:A5A48044-C125-435C-8C6B-806FCBE2DA91@genome.wustl.edu"
type="cite">
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charset=ISO-8859-1">
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<div>
<div style="margin-top: 0px; margin-right: 0px; margin-bottom:
0px; margin-left: 0px;">Hello, </div>
<div style="word-wrap: break-word; -webkit-nbsp-mode: space;
-webkit-line-break: after-white-space; ">
<div>
<div bgcolor="#FFFFFF" text="#000000">
<div class="moz-forward-container">
<div><br>
</div>
<div>I submitted the inquiry (below) to
Miguel Pignatelli and he suggested that I forward
the question to you. Upon looking at our error
messages, he suspects we're having an issue
connecting with the database or else it may be a
general API issue. I've attached the script that we
are attempting to use.</div>
<div><br>
</div>
<div>Thank you for your assistance -</div>
<div>Mike Montague</div>
<table class="moz-email-headers-table"
style="position: static; z-index: auto; " border="0"
cellpadding="0" cellspacing="0">
<tbody>
<tr>
<td>____________</td>
</tr>
</tbody>
</table>
<div apple-content-edited="true"><span
class="Apple-style-span" style="border-collapse:
separate; border-spacing: 0px; "><span
class="Apple-style-span" style="border-collapse:
separate; border-spacing: 0px; ">
<div style="word-wrap: break-word;
-webkit-nbsp-mode: space; -webkit-line-break:
after-white-space; "><br>
Michael J. Montague, Ph.D.<br>
Post-Doctoral Research Associate<br>
The Genome Institute, Washington University
School of Medicine<br>
4444 Forest Park Avenue, Campus Box 8501<br>
St. Louis, MO 63108<br>
T. 718.809.4093<br>
</div>
<div><br>
</div>
</span></span></div>
</div>
</div>
<div>Hello Miguel,</div>
</div>
<div><br>
</div>
<div>With the release of Cafe.v3, we intend to use your
script to obtain data from Ensembl for input into Cafe. We
are interested in gene expansion outliers for the cat
lineage (ID 9685) relative to Carnivora (ID 33554).</div>
<div><br>
</div>
<div>We made a copy of get_expansions.pl (attached below)
and added line 10 to call on the Ensembl API here at the
Genome Institute. It seems to load fine (line 28).</div>
<div><br>
</div>
<blockquote style="margin: 0px 0px 0px 40px; border: none;
padding: 0px; ">L10: <span style="font-family: Menlo;
font-size: 11px; color: rgb(187, 44, 162); ">use</span><span
style="font-family: Menlo; font-size: 11px; "> lib </span><span
style="color: rgb(209, 47, 27); font-family: Menlo;
font-size: 11px; ">'/gscmnt/sata206/techd/ensembl_api/v70/ensembl/modules'</span><span
style="font-family: Menlo; font-size: 11px; ">;</span></blockquote>
<br>
The human adapter loads fine (line 33) but we're wondering
what it has to do with cat?</div>
<div style="word-wrap: break-word; -webkit-nbsp-mode: space;
-webkit-line-break: after-white-space; "><br>
</div>
</div>
</div>
<blockquote style="margin: 0 0 0 40px; border: none; padding:
0px;">
<div>
<div>
<div style="word-wrap: break-word; -webkit-nbsp-mode: space;
-webkit-line-break: after-white-space; "><span
style="font-family: Menlo; font-size: 11px; ">L33: </span><span
style="font-family: Menlo; font-size: 11px; color:
rgb(187, 44, 162); ">my </span><span style="font-family:
Menlo; font-size: 11px; ">$human_gene_adaptor =
$reg->get_adaptor(</span><span style="font-family:
Menlo; font-size: 11px; color: rgb(209, 47, 27); ">"Homo
sapiens"</span><span style="font-family: Menlo;
font-size: 11px; ">, </span><span style="font-family:
Menlo; font-size: 11px; color: rgb(209, 47, 27); ">"core"</span><span
style="font-family: Menlo; font-size: 11px; ">, </span><span
style="font-family: Menlo; font-size: 11px; color:
rgb(209, 47, 27); ">"Gene"</span><span
style="font-family: Menlo; font-size: 11px; ">);</span></div>
</div>
</div>
</blockquote>
<div>
<div style="word-wrap: break-word; -webkit-nbsp-mode: space;
-webkit-line-break: after-white-space; "><br>
</div>
<div style="word-wrap: break-word; -webkit-nbsp-mode: space;
-webkit-line-break: after-white-space; ">The problem is with
line 35, which returns nothing so it crashes in lines 38, 39
and 40.</div>
<div style="word-wrap: break-word; -webkit-nbsp-mode: space;
-webkit-line-break: after-white-space; "><br>
</div>
<div style="word-wrap: break-word; -webkit-nbsp-mode: space;
-webkit-line-break: after-white-space; ">
<blockquote style="margin: 0px 0px 0px 40px; border: none;
padding: 0px; ">
<div>
<div style="word-wrap: break-word; -webkit-nbsp-mode:
space; -webkit-line-break: after-white-space; ">
<div style="margin: 0px; font-size: 11px; font-family:
Menlo; ">
<div style="margin: 0px; ">L35: <span style="color:
rgb(187, 44, 162); ">my</span> $comparaDBA =
Bio::EnsEMBL::Registry->get_DBAdaptor(<span
style="color: rgb(209, 47, 27); ">'Multi'</span>, <span
style="color: rgb(209, 47, 27); ">'compara'</span>);</div>
<div style="margin: 0px; ">
<div style="margin: 0px; ">L38: <span style="color:
#bb2ca2">my</span> $gene_member_adaptor =
$comparaDBA->get_GeneMemberAdaptor;</div>
</div>
</div>
</div>
</div>
</blockquote>
<div style="word-wrap: break-word; -webkit-nbsp-mode: space;
-webkit-line-break: after-white-space; "><br>
</div>
Error:<br>
<blockquote style="margin: 0px 0px 0px 40px; border: none;
padding: 0px; ">
<div><br>
</div>
<div>test_get_expansions.pl 9685 > cat_expansions.txt</div>
<div><br>
</div>
<div>Can't call method "get_GeneMemberAdaptor" on an
undefined value at
/gscuser/mmontagu/bin/test_get_expansions.pl line 38.</div>
<div>cafe_output$ </div>
<div><br>
</div>
</blockquote>
or
<div><br>
</div>
<blockquote style="margin: 0px 0px 0px 40px; border: none;
padding: 0px; ">
<div>perl ~/bin/test_get_expansions.pl 9685 >
cat_expansions.txt</div>
<div><br>
</div>
<div>DBD::mysql::db selectall_arrayref failed: Can't read
dir of '.' (errno: 24) at
/gscmnt/sata206/techd/ensembl_api/v70/ensembl/modules/Bio/EnsEMBL/Registry.pm
line 1600.</div>
<div><br>
</div>
<div>-------------------- WARNING ----------------------</div>
<div>MSG: Homo sapiens is not a valid species name (check DB
and API version)</div>
<div>FILE: Bio/EnsEMBL/Registry.pm LINE: 1187</div>
<div>CALLED BY: Bio/EnsEMBL/Registry.pm LINE: 972</div>
<div>Date (localtime) = Wed Jul 24 14:14:00 2013</div>
<div>Ensembl API version = 70</div>
<div>---------------------------------------------------</div>
<div><br>
</div>
<div>-------------------- EXCEPTION --------------------</div>
<div>MSG: Can not find internal name for species 'Homo
sapiens'</div>
<div>STACK Bio::EnsEMBL::Registry::get_adaptor
/gscmnt/sata206/techd/ensembl_api/v70/ensembl/modules/Bio/EnsEMBL/Registry.pm:974</div>
<div>STACK toplevel
/gscuser/mmontagu/bin/test_get_expansions.pl:33</div>
<div>Date (localtime) = Wed Jul 24 14:14:00 2013</div>
<div>Ensembl API version = 70</div>
<div>---------------------------------------------------</div>
</blockquote>
<div><br>
Mainly, we were wondering if the inputs for lines 33 and 35
are correct for cat? </div>
</div>
</div>
<blockquote style="margin: 0 0 0 40px; border: none; padding:
0px;">
<div>
<div style="word-wrap: break-word; -webkit-nbsp-mode: space;
-webkit-line-break: after-white-space; ">
<div>
<div style="margin: 0px; font-size: 11px; font-family:
Menlo; "><br>
</div>
</div>
</div>
</div>
</blockquote>
<div>
<div style="word-wrap: break-word; -webkit-nbsp-mode: space;
-webkit-line-break: after-white-space; ">
<div>Or alternatively, are we calling on an incorrect version
of the API? Or, perhaps were overlooking something else
altogether?
<div><br>
</div>
</div>
</div>
</div>
<br>
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<div><br class="Apple-interchange-newline">
<blockquote type="cite">
<div style="margin: 0px; "><b>From: </b><a
moz-do-not-send="true" href="mailto:mp@ebi.ac.uk">mp@ebi.ac.uk</a><br>
</div>
<div style="margin: 0px; "><b>Subject: </b><b>Re: Inquiry:
Cafe.v3 Input</b><br>
</div>
<div style="margin: 0px; "><b>Date: </b>July 27, 2013
9:28:02 AM CDT<br>
</div>
<div style="margin: 0px; "><b>To: </b>"Mike Montague" <<a
moz-do-not-send="true"
href="mailto:mmontagu@genome.wustl.edu">mmontagu@genome.wustl.edu</a>><br>
</div>
<div style="margin: 0px; "><b>Cc: </b><a
moz-do-not-send="true" href="mailto:mp@ebi.ac.uk">mp@ebi.ac.uk</a>,
"Wes Warren" <<a moz-do-not-send="true"
href="mailto:wwarren@genome.wustl.edu">wwarren@genome.wustl.edu</a>></div>
</blockquote>
</div>
<div><br>
</div>
<div>
<blockquote type="cite">Dear Mike,<br>
<br>
I am out of the office for some weeks with very limited
access to the<br>
internet at the moment. Looking at your error, it looks
like the problem<br>
is trying to connect with the DB or a general ensembl API
problem. I don't<br>
have at hand the script, but if you can send the
interesting parts to<br>
<a moz-do-not-send="true"
href="mailto:ensembl-dev@ebi.ac.uk">ensembl-dev@ebi.ac.uk</a> you
may be able to find a useful answer in short<br>
time.<br>
I will take a look as soon as I can once I am back.<br>
<br>
Cheers,<br>
<br>
M;</blockquote>
</div>
<blockquote type="cite">
<div><br>
</div>
<div><br>
</div>
<div>
<div style="margin: 0px; "><b>From: </b>Wes Warren <<a
moz-do-not-send="true"
href="mailto:wwarren@genome.wustl.edu">wwarren@genome.wustl.edu</a>><br>
</div>
<div style="margin: 0px; "><b>Subject: </b><b>Fwd: Re:
Fwd: dN/dS</b><br>
</div>
<div style="margin: 0px; "><b>Date: </b>July 9, 2013
1:48:47 PM CDT<br>
</div>
<div style="margin: 0px; "><b>To: </b>Mike Montague <<a
moz-do-not-send="true"
href="mailto:mmontagu@genome.wustl.edu">mmontagu@genome.wustl.edu</a>><br>
</div>
<br>
<div bgcolor="#FFFFFF" text="#000000">Mike,<br>
<br>
The scripts you will need to retrieve cat data for
cafe3. For cafe3 you need 1) a data file containing<br>
gene family sizes for the taxa included in the tree and
2) a Newick formatted tree, including branch lengths for
each gene family. <br>
<br>
Wes<br>
<br>
-------- Original Message -------
<div class="moz-forward-container">
<table class="moz-email-headers-table"
style="position: static; z-index: auto; " border="0"
cellpadding="0" cellspacing="0">
<tbody>
<tr>
<th align="RIGHT" nowrap="nowrap"
valign="BASELINE">Subject:</th>
<td>Re: Fwd: dN/dS</td>
</tr>
<tr>
<th align="RIGHT" nowrap="nowrap"
valign="BASELINE">Date:</th>
<td>Fri, 08 Mar 2013 17:24:06 +0000</td>
</tr>
<tr>
<th align="RIGHT" nowrap="nowrap"
valign="BASELINE">From:</th>
<td>Miguel Pignatelli <a moz-do-not-send="true"
class="moz-txt-link-rfc2396E"
href="mailto:mp@ebi.ac.uk"><mp@ebi.ac.uk></a></td>
</tr>
<tr>
<th align="RIGHT" nowrap="nowrap"
valign="BASELINE">To:</th>
<td>Wes Warren <a moz-do-not-send="true"
class="moz-txt-link-rfc2396E"
href="mailto:wwarren@genome.wustl.edu"><wwarren@genome.wustl.edu></a></td>
</tr>
<tr>
<th align="RIGHT" nowrap="nowrap"
valign="BASELINE">CC:</th>
<td>Javier Herrero <a moz-do-not-send="true"
class="moz-txt-link-rfc2396E"
href="mailto:jherrero@ebi.ac.uk"><jherrero@ebi.ac.uk></a>,
Matthieu Muffato <a moz-do-not-send="true"
class="moz-txt-link-rfc2396E"
href="mailto:muffato@ebi.ac.uk"><muffato@ebi.ac.uk></a></td>
</tr>
</tbody>
</table>
<br>
<br>
<pre>Hi Wes,
The CAFE data is stored in the compara database and is accessible via
the compara API.
I am sending you a file with the 43 genes expanded in cat with respect
to the carnivora taxon.
The columns in the file are:
gene_tree_root_id, gene names, number of members in cat, number of
members in the parent (carnivora), newick format of the species tree.
A couple of comments about this data:
- The newick tree contains the species names and the taxon_ids for the
internal nodes. The numbers are the number of members for each taxon.
- I have only considered significant expansions as reported by our CAFE
analysis. It would be possible to include genes in the "grey" zone (i.e.
genes with more members in cat vs carnivora, but the change not being
significant).
I am also sending you the script I have written to retrieve the data. It
accepts a taxon_id as input. I called it as follows:
$ perl get_expansions.pl 9685 > cat_expansions.txt
If you run the script with other taxon_ids, be aware that it also
reports genes for which the lowest common ancestor is the taxon_id of
interest (i.e. births at the taxon_id of interest).
Let me know if you have any doubt or need further help in getting the
data you want.
Cheers,
M;
On 07/03/13 20:15, Wes Warren wrote:
> Hi Miguel,
>
> Is this data available for cat? All the gene trees are available so I
> assume so but I am not sure where to find the CAFE files.
>
> Thanks,
> Wes
>
> On 3/7/13 12:15 PM, Javier Herrero wrote:
>> Hi Wes
>>
>> This is a question for Miguel, our CAFE expert.
>>
>> Javier
>>
>> On 06/03/13 17:00, Wes Warren wrote:
>>> Is the CAFE output available for cat? We are interested in gene
>>> expansion outliers for the cat lineage, perhaps correlating these
>>> with carnivora.
>>>
>>> Wes
>>></pre>
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