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Added ability to include nodes marked as obsolete #15

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merged 6 commits into from
Sep 27, 2020
+32 −5
Merged

Added ability to include nodes marked as obsolete #15

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11a16d5
Added ability to include nodes marked as obsolete
torstees Sep 25, 2020
94b1c72
Add tests to verify presence or absence of obsolete nodes
torstees Sep 26, 2020
a41940f
Reverted back to nodes for test_read_taxrank_file and switched to loc…
torstees Sep 26, 2020
eccf8b4
Changed the branching criterion to be a little more clear for ignorin…
torstees Sep 26, 2020
bba4310
Skipping version 1 of networkx due to lack of support for nodes function
torstees Sep 26, 2020
159001f
Fixed test_read_taxrank_file to accomodate the recent changes to netw…
torstees Sep 26, 2020
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7 changes: 5 additions & 2 deletions obonet/read.py
100644 → 100755
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@
from .io import open_read_file


def read_obo(path_or_file):
def read_obo(path_or_file, ignore_obsolete=True):
"""
Return a networkx.MultiDiGraph of the ontology serialized by the
specified path or file.
Expand All @@ -19,6 +19,9 @@ def read_obo(path_or_file):
path_or_file : str or file
Path, URL, or open file object. If path or URL, compression is
inferred from the file extension.
ignore_obsolete : boolean
When true (default), terms that are marked 'is_obsolete' will
not be added to the graph.
"""
obo_file = open_read_file(path_or_file)
typedefs, terms, instances, header = get_sections(obo_file)
Expand All @@ -32,7 +35,7 @@ def read_obo(path_or_file):
edge_tuples = list()

for term in terms:
is_obsolete = term.get('is_obsolete', 'false') == 'true'
is_obsolete = ignore_obsolete and term.get('is_obsolete', 'false') == 'true'
if is_obsolete:
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perhaps keep is_obsolete = term.get('is_obsolete', 'false') == 'true' but change the next line to:

if ignore_obsolete and is_obsolete:

continue
term_id = term.pop('id')
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