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Merge relationships, add exception handler
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@tanksha
tanksha committed Apr 20, 2020
1 parent 292e564 commit e0c96ed
Showing 1 changed file with 55 additions and 38 deletions.
93 changes: 55 additions & 38 deletions go-plus.py
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Original file line number Diff line number Diff line change
Expand Up @@ -88,44 +88,61 @@ def inheritLink(term1 , term2, parent_chebis=[]):

print("Started importing")
for i in range(len(df)):
term = get_term(df.iloc[i]["Class ID"])
obsolete = df.iloc[i]["Obsolete"]
definition = df.iloc[i]["definition"]
if obsolete != "true" and "GO" in term:
go.write(evaLink(term, get_term(df.iloc[i]["Preferred Label"]), "has_name"))
go_with_def.write(evaLink(term, get_term(df.iloc[i]["Preferred Label"]), "has_name"))
go_with_def.write(evaLink(term, definition, "GO_definition"))
for col in go_columns:
go.write(evaLink(term, get_term(df.iloc[i][col]), "GO_{}".format(col.replace(" ", "_"))))
go_with_def.write(evaLink(term, get_term(df.iloc[i][col]), "GO_{}".format(col.replace(" ", "_"))))

elif obsolete != "true" and "UBERON" in term:
uberon.write(evaLink(term, get_term(df.iloc[i]["Preferred Label"]), "has_name"))
uberon_with_def.write(evaLink(term, get_term(df.iloc[i]["Preferred Label"]), "has_name"))
uberon_with_def.write(evaLink(term, definition, "UBERON_definition"))
for col in uberon_columns:
uberon.write(evaLink(term, get_term(df.iloc[i][col]), "UBERON_{}".format(col.replace(" ", "_"))))

elif obsolete != "true" and "CL" in term or "ChEBI" in term:
if "CL" in term:
file_name = cl
file_name_with_def = cl_with_def
else:
file_name = chebi
file_name_with_def = chebi_with_def

file_name.write(evaLink(term, get_term(df.iloc[i]["Preferred Label"]), "has_name", parent_chebis=parent_chebis))
file_name_with_def.write(evaLink(term, get_term(df.iloc[i]["Preferred Label"]), "has_name",parent_chebis=parent_chebis))
file_name_with_def.write(evaLink(term, definition, "has_definition", parent_chebis=parent_chebis))
for col in cl_columns:
if col == "Parents":
parents = df.iloc[i][col]
if str(parents) != "nan":
for p in parents.split("|"):
file_name.write(inheritLink(term,get_term(p), parent_chebis=parent_chebis))
file_name_with_def.write(inheritLink(term, get_term(p), parent_chebis=parent_chebis))
try:
term = get_term(df.iloc[i]["Class ID"])
obsolete = df.iloc[i]["Obsolete"]
definition = df.iloc[i]["definition"]
if obsolete != "true" and "GO" in term:
go.write(evaLink(term, get_term(df.iloc[i]["Preferred Label"]), "GO_name"))
go_with_def.write(evaLink(term, get_term(df.iloc[i]["Preferred Label"]), "GO_name"))
go_with_def.write(evaLink(term, definition, "GO_definition"))
for col in go_columns:
"""
positive/negatively regulated by is inverse of positive/negatively regulates
has part is inverse of part of, keep the predicate the same with reverse order
"""
if col.endswith("regulated by"):
col_pred = col.replace("regulated by", "regulates")
go.write(evaLink(get_term(df.iloc[i][col]),term, "GO_{}".format(col_pred.replace(" ", "_"))))
go_with_def.write(evaLink(get_term(df.iloc[i][col]), term, "GO_{}".format(col.replace(" ", "_"))))
elif col == "part of":
col_pred = "has part"
go.write(evaLink(get_term(df.iloc[i][col]), term, "GO_{}".format(col_pred.replace(" ", "_"))))
go_with_def.write(evaLink(get_term(df.iloc[i][col]), term, "GO_{}".format(col.replace(" ", "_"))))
else:
go.write(evaLink(term, get_term(df.iloc[i][col]), "GO_{}".format(col.replace(" ", "_"))))
go_with_def.write(evaLink(term, get_term(df.iloc[i][col]), "GO_{}".format(col.replace(" ", "_"))))

elif obsolete != "true" and "UBERON" in term:
uberon.write(evaLink(term, get_term(df.iloc[i]["Preferred Label"]), "has_name"))
uberon_with_def.write(evaLink(term, get_term(df.iloc[i]["Preferred Label"]), "has_name"))
uberon_with_def.write(evaLink(term, definition, "UBERON_definition"))
for col in uberon_columns:
uberon.write(evaLink(term, get_term(df.iloc[i][col]), "UBERON_{}".format(col.replace(" ", "_"))))

elif obsolete != "true" and "CL" in term or "ChEBI" in term:
if "CL" in term:
file_name = cl
file_name_with_def = cl_with_def
else:
file_name.write(evaLink(term, get_term(df.iloc[i][col]), col.replace(" ", "_"), parent_chebis=parent_chebis))
file_name_with_def.write(evaLink(term, get_term(df.iloc[i][col]), col.replace(" ", "_"), parent_chebis=parent_chebis))
file_name = chebi
file_name_with_def = chebi_with_def

file_name.write(evaLink(term, get_term(df.iloc[i]["Preferred Label"]), "has_name", parent_chebis=parent_chebis))
file_name_with_def.write(evaLink(term, get_term(df.iloc[i]["Preferred Label"]), "has_name",parent_chebis=parent_chebis))
file_name_with_def.write(evaLink(term, definition, "has_definition", parent_chebis=parent_chebis))
for col in cl_columns:
if col == "Parents":
parents = df.iloc[i][col]
if str(parents) != "nan":
for p in parents.split("|"):
file_name.write(inheritLink(term,get_term(p), parent_chebis=parent_chebis))
file_name_with_def.write(inheritLink(term, get_term(p), parent_chebis=parent_chebis))
else:
file_name.write(evaLink(term, get_term(df.iloc[i][col]), col.replace(" ", "_"), parent_chebis=parent_chebis))
file_name_with_def.write(evaLink(term, get_term(df.iloc[i][col]), col.replace(" ", "_"), parent_chebis=parent_chebis))
except Exception as e:
print(e)
continue
print("Done")

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