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Reorganize data.
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Remove YMDBXXX_transposed and change allConcData.xlsx to csv format.
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cheng-yu-zhang committed Apr 24, 2024
1 parent 8eeea35 commit ed2f0b6
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4 changes: 2 additions & 2 deletions add_conc/code/get_YMDB_data.py
Original file line number Diff line number Diff line change
Expand Up @@ -38,8 +38,8 @@ def extract_data(i):
df_transposed.columns = ['Key', 'Content']

# Save the transposed DataFrame to a new Excel file
transposed_excel_path = f'../data/YMDB/{cmp}_transposed.xlsx'
df_transposed.to_excel(transposed_excel_path, index=False, header=True)
transposed_excel_path = f'../data/YMDB/{cmp}_transposed.csv'
df_transposed.to_csv(transposed_excel_path, index=False, header=True)
print(f'Transposed data saved to {transposed_excel_path}')
time.sleep(5)

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34 changes: 6 additions & 28 deletions add_conc/code/organise_data.py
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@@ -1,7 +1,7 @@
####################################################################
# get concentration
# The concentration range is calculated according to the following logic
# For example: In YMDB, three conc is recorded for glutamine ('17140.0 ± 1971.0 umol/L', '2500.0 ± 500.0 umol/L', '15000.0 ± 0.0 umol/L')
# For example: In YMDB, three conc are recorded for glutamine ('17140.0 ± 1971.0 umol/L', '2500.0 ± 500.0 umol/L', '15000.0 ± 0.0 umol/L')
# maximal conc: The maximum concentration plus the corresponding error. In this case, is "17140.0 + 1971.0 umol/L"
# minimal conc: The minimum concentration minus the corresponding error. In this case, is "2500.0 - 500.0 umol/L"

Expand Down Expand Up @@ -46,8 +46,8 @@ def get_conc(rawconc):
print(fn)
# data.to_csv(r'../data/allConcData.csv')

# compute maximal conc and minimal conc
conc = pd.DataFrame(index=['conc', 'maxConc', 'minConc'], columns=data.columns)
# compute maximal conc, minimal conc and mean conc
conc = pd.DataFrame(index=['conc', 'maxConc', 'minConc', 'meanConc'], columns=data.columns)
for i in range(len(data.columns)):
print(i)
rawconc = data.iloc[44, i]
Expand All @@ -56,33 +56,11 @@ def get_conc(rawconc):
conc.loc['conc', data.columns[i]] = all_conc
conc.loc['maxConc', data.columns[i]] = np.max(maxmin)
conc.loc['minConc', data.columns[i]] = np.min(maxmin)
conc.loc['meanConc', data.columns[i]] = np.mean(maxmin)
else:
pass

data = pd.concat([data, conc], axis=0)
newdata = data.loc[['name', 'chebi_id', 'kegg_id', 'conc', 'maxConc', 'minConc']]
newdata = data.loc[['name', 'chebi_id', 'kegg_id', 'conc', 'maxConc', 'minConc', 'meanConc']]
cleaned_data = newdata.dropna(axis=1, subset=['conc'])
cleaned_data.to_excel('../data/allConcData.xlsx')
# # test unit
#
# def check_unit(rawconc):
# concSplit = rawconc.split('}, ')
# unit = []
# try:
# for c in concSplit:
# regex = r'\'([^\']*)\''
# result = re.findall(regex, c)
# unit.append(result[5])
# except:
# pass
# return unit
#
# all_unit= []
# for i in range(len(data.columns)):
# rawconc = data.iloc[44, i]
# unit = check_unit(rawconc)
# for u in unit:
# if u not in all_unit:
# all_unit.append(u)
# print(data.columns[i])
# print(u)
cleaned_data.to_csv('../data/allConcData.csv')
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