def get_analysis_id(self,options):
selections=""; where_clause=""
if options["INSTRUMENT"]:
firstpart, secondpart = add_parameters.selections_conditions("INSTRUMENT", options["INSTRUMENT"], selections); selections="," + firstpart; where_clause+=" and " +secondpart
if options["PAIR"]:
firstpart, secondpart = add_parameters.selections_conditions("PAIR", options["PAIR"], selections); selections="," + firstpart; where_clause+=" and " +secondpart
if options["LANE"]:
firstpart, secondpart = add_parameters.selections_conditions("LANE", options["LANE"], selections); selections="," + firstpart; where_clause+=" and " +secondpart
if options["BARCODE"]:
if os.path.exists(options["BARCODE"]):
list_of_barcodes=read_file.read_file(options["BARCODE"])
else:
list_of_barcodes=options["BARCODE"]
firstpart, secondpart = add_parameters.selections_conditions("BARCODE", list_of_barcodes, selections); selections="," + firstpart; where_clause+=" and " +secondpart
if options["SAMPLE_NAME"]:
if os.path.exists(options["SAMPLE_NAME"]):
list_of_samplenames=read_file.read_file(options["SAMPLE_NAME"])
else:
list_of_samplenames=options["SAMPLE_NAME"]
firstpart, secondpart = add_parameters.selections_conditions("SAMPLE_NAME", list_of_samplenames, selections); selections="," + firstpart; where_clause+=" and " +secondpart
statement = "SELECT analysis_id FROM run WHERE " + where_clause[5:]
statement = statement + " GROUP BY analysis_id"
return self.execute_and_return(statement)
def get_analysis_id(self, options):
selections = ""
where_clause = ""
if options["INSTRUMENT"]:
firstpart, secondpart = add_parameters.selections_conditions(
"INSTRUMENT", options["INSTRUMENT"], selections)
selections = "," + firstpart
where_clause += " and " + secondpart
if options["PAIR"]:
firstpart, secondpart = add_parameters.selections_conditions(
"PAIR", options["PAIR"], selections)
selections = "," + firstpart
where_clause += " and " + secondpart
if options["LANE"]:
firstpart, secondpart = add_parameters.selections_conditions(
"LANE", options["LANE"], selections)
selections = "," + firstpart
where_clause += " and " + secondpart
if options["BARCODE"]:
if os.path.exists(options["BARCODE"]):
list_of_barcodes = read_file.read_file(options["BARCODE"])
else:
list_of_barcodes = options["BARCODE"]
firstpart, secondpart = add_parameters.selections_conditions(
"BARCODE", list_of_barcodes, selections)
selections = "," + firstpart
where_clause += " and " + secondpart
if options["SAMPLE_NAME"]:
if os.path.exists(options["SAMPLE_NAME"]):
list_of_samplenames = read_file.read_file(
options["SAMPLE_NAME"])
else:
list_of_samplenames = options["SAMPLE_NAME"]
firstpart, secondpart = add_parameters.selections_conditions(
"SAMPLE_NAME", list_of_samplenames, selections)
selections = "," + firstpart
where_clause += " and " + secondpart
statement = "SELECT analysis_id FROM run WHERE " + where_clause[5:]
statement = statement + " GROUP BY analysis_id"
return self.execute_and_return(statement)
else:
list_of_ids = options["ids"]
reports = Reports.Reports(config)
tables = reports.get_properties_for_analysis_ids(list_of_ids)
display_outputs(tables)
reports.disconnect()
else:
print "Please provide a list of analysis ids which you wish to get the properties"
exit(1)
elif options["get_barcodes_for_sample_name"]:
if options["SAMPLE_NAME"]:
if os.path.exists(options["SAMPLE_NAME"]):
#read the file
list_of_samplenames = read_file.read_file(options["SAMPLE_NAME"])
selections, where_clause = add_parameters.selections_conditions(
"sample_name", list_of_samplenames, "")
else:
selections, where_clause = add_parameters.selections_conditions(
"sample_name", options["SAMPLE_NAME"], "")
statement = "select distinct run.sample_name, run.barcode from run where " + where_clause + " group by barcode"
reports = Reports.Reports(config)
tables = reports.get_sample_name_for_barcode(statement)
display_outputs(tables)
reports.disconnect()
else:
print "Please provide a sample name to get the barcode for it"
exit(1)
elif options["get_sample_name_for_barcode"]:
if options["BARCODE"]:
if os.path.exists(options["BARCODE"]):
if options["ids"]:
if os.path.exists(options["ids"]):
list_of_ids=read_file.read_file(options["ids"])
else:
list_of_ids=options["ids"]
reports = Reports.Reports(config);tables=reports.get_properties_for_analysis_ids(list_of_ids); display_outputs(tables); reports.disconnect()
else:
print "Please provide a list of analysis ids which you wish to get the properties"
exit(1)
elif options["get_barcodes_for_sample_name"]:
if options["SAMPLE_NAME"]:
if os.path.exists(options["SAMPLE_NAME"]):
#read the file
list_of_samplenames=read_file.read_file(options["SAMPLE_NAME"])
selections, where_clause=add_parameters.selections_conditions("sample_name", list_of_samplenames, "")
else:
selections, where_clause=add_parameters.selections_conditions("sample_name", options["SAMPLE_NAME"], "")
statement = "select distinct run.sample_name, run.barcode from run where " + where_clause + " group by barcode"
reports = Reports.Reports(config);tables=reports.get_sample_name_for_barcode(statement); display_outputs(tables); reports.disconnect()
else:
print "Please provide a sample name to get the barcode for it"
exit(1)
elif options["get_sample_name_for_barcode"]:
if options["BARCODE"]:
if os.path.exists(options["BARCODE"]):
#read the file
list_of_barcodes=read_file.read_file(options["BARCODE"])
selections, where_clause=add_parameters.selections_conditions("barcode", list_of_barcodes, "")
else:
