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feat: include formula for metabolites #5

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Jun 26, 2019
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7 changes: 4 additions & 3 deletions src/metanetx/data.py
Original file line number Diff line number Diff line change
Expand Up @@ -93,9 +93,10 @@ def parse_equation(equation_string):


class Metabolite:
def __init__(self, mnx_id, name):
def __init__(self, mnx_id, name, formula):
self.mnx_id = mnx_id
self.name = name
self.formula = formula

@property
def annotation(self):
Expand Down Expand Up @@ -161,8 +162,8 @@ def load_metanetx_data():
logger.info(f"Loaded {len(reaction_xrefs)} reaction cross-references")

for line in _iterate_tsv(gzip.open("data/chem_prop.tsv.gz", "rt")):
mnx_id, name, _, _, _, _, _, _, _ = line.rstrip("\n").split("\t")
metabolites[mnx_id] = Metabolite(mnx_id, name)
mnx_id, name, formula, _, _, _, _, _, _ = line.rstrip("\n").split("\t")
metabolites[mnx_id] = Metabolite(mnx_id, name, formula)
logger.info(f"Loaded {len(metabolites)} metabolites")

for line in _iterate_tsv(gzip.open("data/chem_xref.tsv.gz", "rt")):
Expand Down
1 change: 1 addition & 0 deletions src/metanetx/schemas.py
Original file line number Diff line number Diff line change
Expand Up @@ -49,6 +49,7 @@ class EquationSchema(Schema):
class MetaboliteSchema(Schema):
mnx_id = fields.Str()
name = fields.Str()
formula = fields.Str()
annotation = fields.Raw()


Expand Down