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author | BonfaceKilz | 2021-04-30 12:26:19 +0300 |
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committer | BonfaceKilz | 2021-04-30 13:45:15 +0300 |
commit | 406eb27859cca232a562c722cbbd37aca2e3be84 (patch) | |
tree | ba3fba783e33cc56c535b68bd64d757bc6cde608 /wqflask/maintenance/quantile_normalize.py | |
parent | c7e661b8ff9f70955418fbc4527378904beb0cf4 (diff) | |
download | genenetwork2-406eb27859cca232a562c722cbbd37aca2e3be84.tar.gz |
autopep8: Fix E301,E302,E303,E304,E305,E306
Diffstat (limited to 'wqflask/maintenance/quantile_normalize.py')
-rw-r--r-- | wqflask/maintenance/quantile_normalize.py | 6 |
1 files changed, 6 insertions, 0 deletions
diff --git a/wqflask/maintenance/quantile_normalize.py b/wqflask/maintenance/quantile_normalize.py index 6751a8e5..1896bc52 100644 --- a/wqflask/maintenance/quantile_normalize.py +++ b/wqflask/maintenance/quantile_normalize.py @@ -14,6 +14,7 @@ from wqflask import app from utility.elasticsearch_tools import get_elasticsearch_connection from utility.tools import ELASTICSEARCH_HOST, ELASTICSEARCH_PORT, SQL_URI + def parse_db_uri(): """Converts a database URI to the db name, host name, user name, and password""" @@ -28,6 +29,7 @@ def parse_db_uri(): print(db_conn_info) return db_conn_info + def create_dataframe(input_file): with open(input_file) as f: ncols = len(f.readline().split("\t")) @@ -36,6 +38,8 @@ def create_dataframe(input_file): return pd.DataFrame(input_array) # This function taken from https://github.com/ShawnLYU/Quantile_Normalize + + def quantileNormalize(df_input): df = df_input.copy() # compute rank @@ -50,6 +54,7 @@ def quantileNormalize(df_input): df[col] = [rank[i] for i in t] return df + def set_data(dataset_name): orig_file = "/home/zas1024/cfw_data/" + dataset_name + ".txt" @@ -95,6 +100,7 @@ def set_data(dataset_name): } } + if __name__ == '__main__': Conn = MySQLdb.Connect(**parse_db_uri()) Cursor = Conn.cursor() |