Mercurial > repos > greg > ensure_synced
view ensure_synced.py @ 4:81232205b179 draft
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author | greg |
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date | Thu, 01 Oct 2020 13:37:48 +0000 |
parents | 2656d87abfee |
children | 68ca17b451f2 |
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#!/usr/bin/env python import argparse import sys import psycopg2 from sqlalchemy import MetaData from sqlalchemy import create_engine 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]) self.affy_ids_from_db.sort() 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()