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authorArthur Centeno2021-06-15 15:33:59 +0000
committerArthur Centeno2021-06-15 15:33:59 +0000
commitc1a6ca69f7c48d99b6c5d62e56a445583fd4c08b (patch)
treef98fccc44829e3f52e585d6b41a1942aa52bd8b7 /wqflask/maintenance/quantile_normalize.py
parent7e49c006af9c4f7453c3578a7d4f1fc4d7bdf3ed (diff)
parent9e9e0e4d440383f617542e810a1115833eafd7bf (diff)
downloadgenenetwork2-c1a6ca69f7c48d99b6c5d62e56a445583fd4c08b.tar.gz
Merge branch 'testing' of github.com:genenetwork/genenetwork2 into acenteno
Diffstat (limited to 'wqflask/maintenance/quantile_normalize.py')
-rw-r--r--wqflask/maintenance/quantile_normalize.py43
1 files changed, 25 insertions, 18 deletions
diff --git a/wqflask/maintenance/quantile_normalize.py b/wqflask/maintenance/quantile_normalize.py
index 701b2b50..0cc963e5 100644
--- a/wqflask/maintenance/quantile_normalize.py
+++ b/wqflask/maintenance/quantile_normalize.py
@@ -14,42 +14,48 @@ 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"""
parsed_uri = urllib.parse.urlparse(SQL_URI)
db_conn_info = dict(
- db = parsed_uri.path[1:],
- host = parsed_uri.hostname,
- user = parsed_uri.username,
- passwd = parsed_uri.password)
+ db=parsed_uri.path[1:],
+ host=parsed_uri.hostname,
+ user=parsed_uri.username,
+ passwd=parsed_uri.password)
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"))
- input_array = np.loadtxt(open(input_file, "rb"), delimiter="\t", skiprows=1, usecols=list(range(1, ncols)))
+ input_array = np.loadtxt(open(
+ input_file, "rb"), delimiter="\t", skiprows=1, usecols=list(range(1, ncols)))
return pd.DataFrame(input_array)
-#This function taken from https://github.com/ShawnLYU/Quantile_Normalize
+# This function taken from https://github.com/ShawnLYU/Quantile_Normalize
+
+
def quantileNormalize(df_input):
df = df_input.copy()
- #compute rank
+ # compute rank
dic = {}
for col in df:
- dic.update({col : sorted(df[col])})
+ dic.update({col: sorted(df[col])})
sorted_df = pd.DataFrame(dic)
- rank = sorted_df.mean(axis = 1).tolist()
- #sort
+ rank = sorted_df.mean(axis=1).tolist()
+ # sort
for col in df:
t = np.searchsorted(np.sort(df[col]), df[col])
df[col] = [rank[i] for i in t]
return df
+
def set_data(dataset_name):
orig_file = "/home/zas1024/cfw_data/" + dataset_name + ".txt"
@@ -64,10 +70,10 @@ def set_data(dataset_name):
trait_name = line1.split('\t')[0]
for i, sample in enumerate(sample_names):
this_sample = {
- "name": sample,
- "value": line1.split('\t')[i+1],
- "qnorm": line2.split('\t')[i+1]
- }
+ "name": sample,
+ "value": line1.split('\t')[i + 1],
+ "qnorm": line2.split('\t')[i + 1]
+ }
sample_list.append(this_sample)
query = """SELECT Species.SpeciesName, InbredSet.InbredSetName, ProbeSetFreeze.FullName
FROM Species, InbredSet, ProbeSetFreeze, ProbeFreeze, ProbeSetXRef, ProbeSet
@@ -95,13 +101,14 @@ def set_data(dataset_name):
}
}
+
if __name__ == '__main__':
Conn = MySQLdb.Connect(**parse_db_uri())
Cursor = Conn.cursor()
- #es = Elasticsearch([{
+ # es = Elasticsearch([{
# "host": ELASTICSEARCH_HOST, "port": ELASTICSEARCH_PORT
- #}], timeout=60) if (ELASTICSEARCH_HOST and ELASTICSEARCH_PORT) else None
+ # }], timeout=60) if (ELASTICSEARCH_HOST and ELASTICSEARCH_PORT) else None
es = get_elasticsearch_connection(for_user=False)
@@ -116,8 +123,8 @@ if __name__ == '__main__':
success, _ = bulk(es, set_data(sys.argv[1]))
response = es.search(
- index = "traits", doc_type = "trait", body = {
- "query": { "match": { "name": "ENSMUSG00000028982" } }
+ index="traits", doc_type="trait", body={
+ "query": {"match": {"name": "ENSMUSG00000028982"}}
}
)