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8 changes: 8 additions & 0 deletions ontobio/ontol_factory.py
Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,7 @@
import os
import subprocess
import hashlib
import fastobo


# TODO
Expand Down Expand Up @@ -155,6 +156,13 @@ def translate_file_to_ontology(handle, **args):
logging.info("RdfMapper: {}".format(args))
m = RdfMapper(**args)
return m.convert(handle,'ttl')
elif handle.endswith(".obo"):
doc = fastobo.load(handle)
with tempfile.TemporaryFile() as tmp:
fastobo.dump_graph(doc, tmp)
tmp.seek(0)
g = obograph_util.convert_json_object(json.load(tmp), **args)
return Ontology(handle=handle, payload=g)
else:
if not (handle.endswith(".obo") or handle.endswith(".owl")):
logging.info("Attempting to parse non obo or owl file with owltools: "+handle)
Expand Down
3 changes: 2 additions & 1 deletion requirements.txt
Original file line number Diff line number Diff line change
Expand Up @@ -19,4 +19,5 @@ pydotplus>=0.0
plotly==2.0.7
pyyaml
yamldown>=0.1.7
click
fastobo~=0.3.1
click
3 changes: 2 additions & 1 deletion setup.py
Original file line number Diff line number Diff line change
Expand Up @@ -56,7 +56,8 @@
'pandas==0.24.2',
'click==7.0',
'yamldown',
'dataclasses'
'dataclasses',
'fastobo~=0.3.1',
],

# List additional groups of dependencies here (e.g. development
Expand Down