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Parse REACTION as a separate field #19

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merged 3 commits into from
Feb 5, 2024
Merged

Parse REACTION as a separate field #19

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3c325ab
move REACTION to its separate field in PARSE_KO to reflect changes to…
sterrettJD Feb 5, 2024
c056fb4
new REACTION field to reflect kegg changes
sterrettJD Feb 5, 2024
658e23c
update REACTION field in KO test
sterrettJD Feb 5, 2024
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5 changes: 3 additions & 2 deletions KEGG_parser/parsers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -154,7 +154,8 @@ def split_module_reaction(current_dict, current_entry_name, current_entry_data):
PARSE_KO_BY_FIELD = {
'ENTRY': split_entry, 'NAME': split_name_by_comma, 'DEFINITION': return_self,
'PATHWAY': split_and_append, 'MODULE': split_and_append, 'DISEASE': split_and_append,
'CLASS': add_class, 'DBLINKS': add_nested_dict, 'GENES': add_nested_dict
'CLASS': add_class, 'DBLINKS': add_nested_dict, 'GENES': add_nested_dict,
'REACTION': split_and_append
}

PARSE_RN_BY_FIELD = {
Expand Down Expand Up @@ -194,7 +195,7 @@ def split_module_reaction(current_dict, current_entry_name, current_entry_data):
'COMPOUND': add_module_orthology, 'COMMENT': return_self, 'DBLINKS': add_nested_dict
}

NOT_CAPTURED_KO_FIELDS = ('REFERENCE', 'AUTHORS', 'TITLE', 'JOURNAL', 'SEQUENCE', 'BRITE', 'SYMBOL', 'REACTION',
NOT_CAPTURED_KO_FIELDS = ('REFERENCE', 'AUTHORS', 'TITLE', 'JOURNAL', 'SEQUENCE', 'BRITE', 'SYMBOL',
'NETWORK', 'ELEMENT')

NOT_CAPTURED_RN_FIELDS = ('REFERENCE', 'AUTHORS', 'TITLE', 'JOURNAL', 'BRITE')
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6 changes: 4 additions & 2 deletions tests/test_fixtures.py
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Expand Up @@ -8,8 +8,10 @@ def ko_raw_record():
"PATHWAY ko00000 a fake pathway\n" \
"DISEASE H00000 A bad one\n" \
"CLASS Metabolism; Carbohydrate Metabolism; Glycolysis / Gluconeogenesis[PATH:ko00010]\n" \
"DBLINKS RN: R00000\n" \
" COG: COG0000\n" \
"REACTION R00623 primary_alcohol:NAD+ oxidoreductase\n" \
" R00754 ethanol:NAD+ oxidoreductase\n" \
"DBLINKS COG: COG0000\n" \
" GO: 0004022 0004023 0004024 0004025\n" \
"GENES HSA: hsa00000\n" \
"REFERENCE\n" \
" AUTHORS Fake G.\n" \
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7 changes: 5 additions & 2 deletions tests/test_parse_KEGG.py
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Expand Up @@ -29,9 +29,12 @@ def test_get_from_kegg_rxns(loop, list_of_rxns):

def test_parse_ko(ko_raw_record):
ko_record = parse_ko(ko_raw_record)
assert len(ko_record) == 8
assert tuple(ko_record['DBLINKS']['RN']) == tuple(['R00000'])
assert len(ko_record) == 9
assert tuple(ko_record['REACTION']) == tuple([('R00623', 'primary_alcohol:NAD+ oxidoreductase'),
('R00754', 'ethanol:NAD+ oxidoreductase')
])
assert tuple(ko_record['DBLINKS']['COG']) == tuple(['COG0000'])
assert tuple(ko_record['DBLINKS']['GO']) == tuple(["0004022", "0004023", "0004024", "0004025"])


@pytest.fixture()
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