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1 #!/usr/bin/env python
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2
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2
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3 import argparse
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4 import sys
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5
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3
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6 import psycopg2
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7
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7 from sqlalchemy import create_engine
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3
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8 from sqlalchemy import MetaData
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9 from sqlalchemy.engine.url import make_url
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10
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11 metadata = MetaData()
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12
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13 SKIP_VALS = ['#CHROM', 'POS', 'ID', 'REF', 'ALT', 'QUAL', 'FILTER', 'INFO', 'FORMAT']
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14
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15
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16 class EnsureSynced(object):
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17 def __init__(self):
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18 self.args = None
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19 self.conn = None
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20 self.parse_args()
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21 self.outfh = open(self.args.output, "w")
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22 self.connect_db()
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23 self.engine = create_engine(self.args.database_connection_string)
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24 self.metadata = MetaData(self.engine)
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8
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25 self.coral_mlg_rep_sample_ids_from_db = []
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26 self.affy_ids_from_file = []
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27
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28 def connect_db(self):
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29 url = make_url(self.args.database_connection_string)
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30 args = url.translate_connect_args(username='user')
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31 args.update(url.query)
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32 assert url.get_dialect().name == 'postgresql', 'This script can only be used with PostgreSQL.'
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33 self.conn = psycopg2.connect(**args)
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34
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35 def get_coral_mlg_rep_sample_ids_from_db(self):
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36 cmd = "SELECT coral_mlg_rep_sample_id, coral_mlg_clonal_id FROM genotype WHERE coral_mlg_rep_sample_id IS NOT NULL AND coral_mlg_rep_sample_id != '' AND coral_mlg_clonal_id != 'failed' ORDER BY coral_mlg_rep_sample_id;"
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37 cur = self.conn.cursor()
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38 cur.execute(cmd)
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39 rows = cur.fetchall()
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40 for row in rows:
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41 self.coral_mlg_rep_sample_ids_from_db.append(row[0])
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42 self.coral_mlg_rep_sample_ids_from_db.sort()
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43
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44 def get_affy_ids_from_file(self, f):
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45 with open(f) as fh:
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46 for line in fh:
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47 line = line.strip()
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48 if line in SKIP_VALS:
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49 # Skip the first 9 lines in the file.
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50 continue
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51 self.affy_ids_from_file.append(line)
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52 self.affy_ids_from_file.sort()
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53
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54 def get_difference(self, list1, list2):
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55 if len(list1) > len(list2):
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56 return list(set(list1) - set(list2))
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57 return list(set(list2) - set(list1))
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58
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59 def log(self, msg):
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60 self.outfh.write("%s\n" % msg)
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61
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62 def parse_args(self):
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63 parser = argparse.ArgumentParser()
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64 parser.add_argument('--database_connection_string', dest='database_connection_string', help='Postgres database connection string'),
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65 parser.add_argument('--affy_ids_from_file', dest='affy_ids_from_file', help='Affy ids taken from all previously genotyped samples vcf file')
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66 parser.add_argument('--output', dest='output', help='Output dataset'),
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67 self.args = parser.parse_args()
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68
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69 def run(self):
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70 self.get_coral_mlg_rep_sample_ids_from_db()
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71 self.get_affy_ids_from_file(self.args.affy_ids_from_file)
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72 if self.coral_mlg_rep_sample_ids_from_db == self.affy_ids_from_file:
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73 in_sync = True
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74 self.log("The selected file is in sync with the database.\n\n")
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75 else:
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76 in_sync = False
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77 self.log("The selected file is not in sync with the database.\n\n")
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78 num_coral_mlg_rep_sample_ids_from_db = len(self.coral_mlg_rep_sample_ids_from_db)
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79 self.log("Number of coral mlg rep sample ids in the database: %d\n" % num_coral_mlg_rep_sample_ids_from_db)
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80 num_affy_ids_from_file = len(self.affy_ids_from_file)
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81 self.log("Number of Affymetrix ids in the file: %d\n" % num_affy_ids_from_file)
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82 if not in_sync:
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83 if num_coral_mlg_rep_sample_ids_from_db > num_affy_ids_from_file:
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84 self.log("The database contains the following Affymetrix ids that are not in the file.\n")
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85 else:
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86 self.log("The file contains the following Affymetrix ids that are not in the database.\n")
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87 diff_list = self.get_difference(self.coral_mlg_rep_sample_ids_from_db, self.affy_ids_from_file)
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88 for affy_id in diff_list:
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89 self.log("%s\n" % affy_id)
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90 self.outfh.flush()
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91 self.outfh.close()
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92 sys.exit(1)
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93
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94 def shutdown(self):
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95 self.outfh.flush()
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96 self.outfh.close()
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97 self.conn.close()
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98
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99
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100 if __name__ == '__main__':
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101 es = EnsureSynced()
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102 es.run()
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103 es.shutdown()
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