Snippets

Dénes Türei Short guide for the annotations and intercell databases in pypath

Updated by Dénes Türei
View revision

File intercell_guide.py Modified

  • Ignore whitespace
  • Hide word diff 
 # Denes Turei
 # turei.denes@gmail.com
 
+import importlib as imp
+
 from pypath import omnipath
+from pypath.core import intercell
+from pypath.core import annot
+from pypath.core import intercell_annot
+from pypath.utils import mapping
 
 a = omnipath.db.get_db('annotations')
 i = omnipath.db.get_db('intercell')
 i.entities_by_resource()
 
 # get all members from one class
-i.get_class('tight_junction')
+i.get_class('tight_junction')
+
+# to see gene symbols
+mapping.map_names(i.get_class('ligand'), 'uniprot', 'genesymbol')
+
+# how to change the annotation definitions
+# -- edit the definition in the pypath/core/intercell_annot.py file in your
+#    local repo
+# -- reload the modules
+# -- rebuild the intercell database
+# -- if you are satisfied with the result, commit your changes with a good
+#    commit message and push it to the origin
+# -- please commit each change separately so we can keep track what's going on
+
+# once you have the definitions changed, reload the modules
+imp.reload(intercell_annot)
+imp.reload(annot)
+imp.reload(intercell)
+
+# rebuild the intercell database (this takes time but is relatively quick
+# as the annotations and complex databases are already loaded and we don't
+# need to change them)
+i = intercell.IntercellAnnotation()
+
+# then inspect the new `i` object if your changes could address the wrong
+# annotations; if you are satisfied commit your changes
Created by Dénes Türei
View revision

File intercell_guide.py Added

  • Ignore whitespace
  • Hide word diff 
+#!/usr/bin/env python
+
+# Saez Lab 2020
+# Denes Turei
+# turei.denes@gmail.com
+
+from pypath import omnipath
+
+a = omnipath.db.get_db('annotations')
+i = omnipath.db.get_db('intercell')
+
+# the annotation database
+
+# individual annotation databases:
+a.annots
+
+# select one database
+comppi = a.annots['ComPPI']
+
+# query the fields
+comppi.get_names()
+
+# query the values for one field
+comppi.get_values('location')
+
+# query the proteins by field-value pairs
+comppi.get_subset(location = 'nucleus')
+comppi.get_subset(location = {'nucleus', 'cytosol'})
+
+# the intercell database
+
+# the category names
+i.class_names
+
+# their labels
+i.class_labels
+
+# get all the classes for a protein
+i.classes_by_entity('P00533')
+
+# count the members in each class
+i.counts_by_class()
+
+# get the entities annotated by each resource
+i.entities_by_resource()
+
+# get all members from one class
+i.get_class('tight_junction')
HTTPS SSH

You can clone a snippet to your computer for local editing. Learn more.