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#!/usr/bin/env python |
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# -*- coding: UTF-8 -*- |
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""" Maps gene associations to a 'slim' ontology. |
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This roughly implements the functionality of the perl script map2slim. |
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See: [http://search.cpan.org/~cmungall/go-perl/scripts/map2slim] |
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For a description of GO Slims look here: |
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http://geneontology.org/GO.slims.shtml |
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For now this does not implement Bucket Terms. |
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""" |
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from .obo_parser import GODag |
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def mapslim(go_term, go_dag, goslim_dag): |
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""" Maps a GO term (accession) to it's GO slim terms. |
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Parameters: |
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- go_term: the accession to be mapped to the slim terms |
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- go_dag: the (full) Gene Ontology DAG |
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- goslim_dag: the GO Slim DAG |
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Returns: |
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Two sets: |
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direct_ancestors, all_ancestors |
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- direct_ancestors: The direct ancestors of the given term that are in |
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the GO Slim. Those are the terms that are not |
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covered by earlier ancestors of the GO Slims in |
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_any_ path (from bottom to top). |
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- all_ancestors: All ancestors of the given term that are part of |
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the GO-Slim terms. |
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""" |
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# check parameters |
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if not isinstance(go_dag, GODag): |
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raise TypeError("go_dag must be an instance of GODag") |
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if not isinstance(goslim_dag, GODag): |
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raise TypeError("goslim_dag must be an instance of GODag") |
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if go_term not in go_dag: |
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raise ValueError("go_term must be an accession that is in the go_dag") |
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all_ancestors = set() |
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covered_ancestors = set() |
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# get all paths for the term in the go_dag |
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paths = go_dag.paths_to_top(go_term) |
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for path in paths: |
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# the next loop needs to run bottom->up, i.e. from the go_term item to |
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# the root, thus we need to reverse the list prior to iteration |
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path.reverse() |
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got_leaf = False |
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for term in path: |
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if term.id in goslim_dag: |
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all_ancestors.add(term.id) |
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if got_leaf: |
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covered_ancestors.add(term.id) |
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got_leaf = True |
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# get the direct ancestors, i.e. those that are not covered by a earlier |
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# ancestor of the GO-Slim in _any_ path (in bottom->top order) |
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direct_ancestors = all_ancestors - covered_ancestors |
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return direct_ancestors, all_ancestors |
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tanghaibao /
goatools
