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<div class="moz-cite-prefix">Hi,<br>
Some time ago I wrote Biopython module for handling Ontologies and
calculating terms enrichments. Here is the module:<br>
<a class="moz-txt-link-freetext" href="https://github.com/kkoziara/biopython/tree/master/Bio/Ontology">https://github.com/kkoziara/biopython/tree/master/Bio/Ontology</a><br>
Bio.Ontology.IO.OboIO contains OboReader which can read the obo
file into OntologyGraph. OntologyGraph contains get_ancestor
method which returns all ancestors of a term. It also contains
to_networkx method which returns networkx representation of
OntologyGraph.<br>
I hope it helps.<br>
Regards,<br>
Kamil<br>
<br>
On 06/14/2014 09:16 PM, Iddo Friedberg wrote:<br>
</div>
<blockquote
cite="mid:CABm4-MQqn3rNkUUZDyouTD_=yPpnb=q+9TBsetJrRMpEGhtx6g@mail.gmail.com"
type="cite">
<div dir="ltr"><span
style="font-family:arial,sans-serif;font-size:13px">hi,</span>
<div style="font-family:arial,sans-serif;font-size:13px"><br>
</div>
<div style="font-family:arial,sans-serif;font-size:13px">Does
anybody have a script that can extract an ancestor list of an
ontology term (or all ontology terms) from an OBO file? Or
something close enough so I can modify it?<br clear="all">
<div><br>
</div>
<div>Thanks,</div>
<div><br>
</div>
<div>Iddo</div>
</div>
<div><br>
</div>
-- <br>
Iddo Friedberg<br>
<a moz-do-not-send="true"
href="http://iddo-friedberg.net/contact.html" target="_blank">http://iddo-friedberg.net/contact.html</a><br>
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++++++..----.<<<<++++++++++++++++++++++++++++.-----------..>>>+.-----.<br>
.>-.<<<<--.>>>++.>+++.<+++.----.-.<++++++++++++++++++.>+.>.<++.<<<+.>><br>
>>----.<--.>++++++.<<<<------------------------------------.<br>
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