diff ensure_synced.py @ 0:9180906544b6 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ensure_synced.py	Thu Aug 15 10:37:49 2019 -0400
@@ -0,0 +1,103 @@
+#!/usr/bin/env python
+from __future__ import print_function
+
+import argparse
+import psycopg2
+import sys
+
+from sqlalchemy import create_engine
+from sqlalchemy import MetaData
+from sqlalchemy.engine.url import make_url
+
+metadata = MetaData()
+
+SKIP_VALS = ['#CHROM', 'POS', 'ID', 'REF', 'ALT', 'QUAL', 'FILTER', 'INFO', 'FORMAT']
+
+
+class EnsureSynced(object):
+    def __init__(self):
+        self.args = None
+        self.conn = None
+        self.parse_args()
+        self.outfh = open(self.args.output, "w")
+        self.connect_db()
+        self.engine = create_engine(self.args.database_connection_string)
+        self.metadata = MetaData(self.engine)
+        self.affy_ids_from_db = []
+        self.affy_ids_from_file = []
+
+    def connect_db(self):
+        url = make_url(self.args.database_connection_string)
+        args = url.translate_connect_args(username='user')
+        args.update(url.query)
+        assert url.get_dialect().name == 'postgresql', 'This script can only be used with PostgreSQL.'
+        self.conn = psycopg2.connect(**args)
+
+    def get_affy_ids_from_db(self):
+        cmd = "SELECT affy_id FROM sample WHERE genotype_id NOT IN (SELECT id FROM genotype WHERE coral_mlg_clonal_id = 'failed') ORDER BY affy_id;"
+        cur = self.conn.cursor()
+        cur.execute(cmd)
+        rows = cur.fetchall()
+        for row in rows:
+            self.affy_ids_from_db.append(row[0])
+
+    def get_affy_ids_from_file(self, f):
+        with open(f) as fh:
+            for line in fh:
+                line = line.strip()
+                if line in SKIP_VALS:
+                    # Skip the first 9 lines in the file.
+                    continue
+                self.affy_ids_from_file.append(line)
+        self.affy_ids_from_file.sort()
+
+    def get_difference(self, list1, list2):
+        if len(list1) > len(list2):
+            return list(set(list1) - set(list2))
+        return list(set(list2) - set(list1))
+
+    def log(self, msg):
+        self.outfh.write("%s\n" % msg)
+
+    def parse_args(self):
+        parser = argparse.ArgumentParser()
+        parser.add_argument('--database_connection_string', dest='database_connection_string', help='Postgres database connection string'),
+        parser.add_argument('--affy_ids_from_file', dest='affy_ids_from_file', help='Affy ids taken from all previously genotyped samples vcf file')
+        parser.add_argument('--output', dest='output', help='Output dataset'),
+        self.args = parser.parse_args()
+
+    def run(self):
+        self.get_affy_ids_from_db()
+        self.get_affy_ids_from_file(self.args.affy_ids_from_file)
+        if self.affy_ids_from_db == self.affy_ids_from_file:
+            in_sync = True
+            self.log("The selected file is in sync with the database.\n\n")
+        else:
+            in_sync = False
+            self.log("The selected file is not in sync with the database.\n\n")
+        num_affy_ids_from_db = len(self.affy_ids_from_db)
+        self.log("Number of Affymetrix ids in the database: %d\n" % num_affy_ids_from_db)
+        num_affy_ids_from_file = len(self.affy_ids_from_file)
+        self.log("Number of Affymetrix ids in the file: %d\n" % num_affy_ids_from_file)
+        if not in_sync:
+            if num_affy_ids_from_db > num_affy_ids_from_file:
+                self.log("The database contains the following Affymetrix ids that are not in the file.\n")
+            else:
+                self.log("The file contains the following Affymetrix ids that are not in the database.\n")
+            diff_list = self.get_difference(self.affy_ids_from_db, self.affy_ids_from_file)
+            for affy_id in diff_list:
+                self.log("%s\n" % affy_id)
+            self.outfh.flush()
+            self.outfh.close()
+            sys.exit(1)
+
+    def shutdown(self):
+        self.outfh.flush()
+        self.outfh.close()
+        self.conn.close()
+
+
+if __name__ == '__main__':
+    es = EnsureSynced()
+    es.run()
+    es.shutdown()