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How to use replicate_key method in localstack

Best Python code snippet using localstack_python

test_parsers.py

Source:test_parsers.py

1import unittest2import impact3import os4import impact.parsers as parsers5BASE_DIR = os.path.dirname(os.path.dirname(os.path.realpath(__file__)))6class TestParsers(unittest.TestCase):7    def test_generic_identifier_parser(self):8        ti = impact.ReplicateTrialIdentifier()9        ti.parse_identifier(10            'time:1|'11            'environment__labware:Falcon96|'12            'environment__shaking_speed:250|'13            'environment__temperature:37|'14            'media__base:LIMS|'15            'media__cc:10 glc__D|'16            'rep:1|'17            'strain__id:D1|'18            'strain__ko:adh,pta,lacI|'19            'strain:MG|'20            'strain__plasmid:pKDL|'21            'strain__plasmid:pKDL3|'22            'strain__plasmid:pKDL2')23        self.assertEqual(ti.time,1.)24        self.assertEqual(ti.environment.labware.name,'Falcon96')25        self.assertEqual(ti.environment.shaking_speed,250)26        self.assertEqual(ti.environment.temperature,37)27        self.assertEqual(ti.media.parent,'LIMS')28        print(ti.media.components)29        self.assertEqual(ti.media.components['glc__D'].component_name,'glc__D')30        self.assertEqual(ti.media.components['glc__D'].concentration,10)31        self.assertEqual(ti.replicate_id,1)32        # self.assertEqual(ti.strain.id,'D1') #TODO update33        self.assertEqual(ti.strain.name,'MG')34        self.assertIn('pKDL',[plasmid.name for plasmid in ti.strain.plasmids])35        self.assertIn('pKDL2',[plasmid.name for plasmid in ti.strain.plasmids])36        self.assertIn('pKDL3',[plasmid.name for plasmid in ti.strain.plasmids])37    def test_default_HPLC_parser(self):38        expt = impact.Experiment()39        parsers.Parser.parse_raw_data(data_format='default_titers', file_name=os.path.join(BASE_DIR, 'tests/test_data/sample_input_data.xlsx'), experiment=expt, id_type='CSV')40        num_replicates = (len(expt.replicate_trial_dict.keys()))41        num_single_trials = len([42            single_trial_key for replicate_key in expt.replicate_trial_dict43            for single_trial_key in expt.replicate_trial_dict[replicate_key].single_trial_dict44        ])45        num_analyte_data = len([46            analyte_name for replicate_key in expt.replicate_trial_dict47            for single_trial_key in expt.replicate_trial_dict[replicate_key].single_trial_dict48            for analyte_name in expt.replicate_trial_dict[replicate_key].single_trial_dict[single_trial_key].analyte_dict49        ])50        num_time_points = len([51            time_point for replicate_key in expt.replicate_trial_dict52            for single_trial_key in expt.replicate_trial_dict[replicate_key].single_trial_dict53            for analyte_name in expt.replicate_trial_dict[replicate_key].single_trial_dict[single_trial_key].analyte_dict54            for time_point in expt.replicate_trial_dict[replicate_key].single_trial_dict[single_trial_key].analyte_dict[analyte_name].time_points55        ])56        self.assertEqual(num_replicates,7)57        self.assertEqual(num_single_trials,18)58        self.assertEqual(num_analyte_data,252)59        self.assertEqual(num_time_points,2884)60    def test_spectromax_parser(self):61        expt = impact.Experiment()62        parsers.Parser.parse_raw_data(data_format='spectromax_OD', id_type='traverse', file_name=os.path.join(BASE_DIR,'tests/test_data/sample_spectromax_data.xlsx'), experiment = expt)63        num_replicates = (len(expt.replicate_trial_dict.keys()))64        num_single_trials = len([65            single_trial_key for replicate_key in expt.replicate_trial_dict66            for single_trial_key in expt.replicate_trial_dict[replicate_key].single_trial_dict67        ])68        num_analyte_data = len([69            analyte_name for replicate_key in expt.replicate_trial_dict70            for single_trial_key in expt.replicate_trial_dict[replicate_key].single_trial_dict71            for analyte_name in expt.replicate_trial_dict[replicate_key].single_trial_dict[single_trial_key].analyte_dict72        ])73        num_time_points = len([74            time_point for replicate_key in expt.replicate_trial_dict75            for single_trial_key in expt.replicate_trial_dict[replicate_key].single_trial_dict76            for analyte_name in expt.replicate_trial_dict[replicate_key].single_trial_dict[single_trial_key].analyte_dict77            for time_point in expt.replicate_trial_dict[replicate_key].single_trial_dict[single_trial_key].analyte_dict[analyte_name].time_points78        ])79        self.assertEqual(num_replicates,32)80        self.assertEqual(num_single_trials,88)81        self.assertEqual(num_analyte_data,88)82        self.assertEqual(num_time_points,880)83    def test_tecan_OD_parser(self):84        expt = impact.Experiment()85        parsers.Parser.parse_raw_data(data_format='tecan', id_type='traverse', file_name=os.path.join(BASE_DIR,'tests/test_data/sample_tecan_OD_data.xlsx'), experiment=expt)86        num_replicates = (len(expt.replicate_trial_dict.keys()))87        num_single_trials = len([88            single_trial_key for replicate_key in expt.replicate_trial_dict89            for single_trial_key in expt.replicate_trial_dict[replicate_key].single_trial_dict90        ])91        num_analyte_data = len([92            analyte_name for replicate_key in expt.replicate_trial_dict93            for single_trial_key in expt.replicate_trial_dict[replicate_key].single_trial_dict94            for analyte_name in expt.replicate_trial_dict[replicate_key].single_trial_dict[single_trial_key].analyte_dict95        ])96        num_time_points = len([97            time_point for replicate_key in expt.replicate_trial_dict98            for single_trial_key in expt.replicate_trial_dict[replicate_key].single_trial_dict99            for analyte_name in expt.replicate_trial_dict[replicate_key].single_trial_dict[single_trial_key].analyte_dict100            for time_point in expt.replicate_trial_dict[replicate_key].single_trial_dict[single_trial_key].analyte_dict[analyte_name].time_points101        ])102        self.assertEqual(num_replicates,56)103        self.assertEqual(num_single_trials,96)104        self.assertEqual(num_analyte_data,96)105        self.assertEqual(num_time_points,960)106    def test_tecan_OD_reporter_parser(self):107        expt = impact.Experiment()108        parsers.Parser.parse_raw_data(data_format='tecan', id_type='traverse',109                                      file_name=os.path.join(BASE_DIR,110                                                             'tests/test_data/sample_tecan_OD_reporter_data.xlsx'),111                                      experiment=expt)112        num_replicates = (len(expt.replicate_trial_dict.keys()))113        num_single_trials = len([114            single_trial_key for replicate_key in expt.replicate_trial_dict115            for single_trial_key in expt.replicate_trial_dict[replicate_key].single_trial_dict116        ])117        num_analyte_data = len([118            analyte_name for replicate_key in expt.replicate_trial_dict119            for single_trial_key in expt.replicate_trial_dict[replicate_key].single_trial_dict120            for analyte_name in121            expt.replicate_trial_dict[replicate_key].single_trial_dict[single_trial_key].analyte_dict122        ])123        num_time_points = len([124            time_point for replicate_key in expt.replicate_trial_dict125            for single_trial_key in expt.replicate_trial_dict[replicate_key].single_trial_dict126            for analyte_name in127            expt.replicate_trial_dict[replicate_key].single_trial_dict[single_trial_key].analyte_dict128            for time_point in129            expt.replicate_trial_dict[replicate_key].single_trial_dict[single_trial_key].analyte_dict[130                analyte_name].time_points131        ])132        self.assertEqual(num_replicates, 56)133        self.assertEqual(num_single_trials, 96)134        self.assertEqual(num_analyte_data, 288)135        self.assertEqual(num_time_points, 2880)136if __name__ == '__main__':...

MM_reducer.py

Source:MM_reducer.py

1#!/usr/bin/env python32import sys3# NUMBER_OF_COLUMNS_IN_A = int(sys.argv[1])4NUMBER_OF_COLUMNS_IN_A = 5005def main():6    current_key = None7    total_sum = 0.08    value_dict = dict()9    # for key_value_pair in key_value_pairs:10    for key_value_pair in sys.stdin:11        key_value_pair = key_value_pair.strip()12        key, value = key_value_pair.split('\t', 1)13        try:14            row_number, column_number = map(int, key.split(','))15            key = (row_number, column_number)16            value = value.split(',')17            replicate_key, element_value = int(value[1]), float(value[2])18        except:19            continue20        if key == current_key:21            if replicate_key not in value_dict:22                value_dict[replicate_key] = [element_value]23            else:24                value_dict[replicate_key].append(element_value)25        else:26            if current_key:27                for i in range(1, NUMBER_OF_COLUMNS_IN_A + 1):28                    if (i in value_dict) and (len(value_dict[i]) == 2):29                        total_sum = total_sum + value_dict[i][0] * value_dict[i][1]30                print('({},{}),{}'.format(current_key[0],31                                          current_key[1],32                                          total_sum,33                                          )34                      )35            current_key = key36            value_dict = dict()37            value_dict[replicate_key] = [element_value]38            total_sum = 0.039    if current_key:40        for j in range(1, NUMBER_OF_COLUMNS_IN_A + 1):41            if (j in value_dict) and (len(value_dict[j]) == 2):42                total_sum = total_sum + value_dict[j][0] * value_dict[j][1]43        print('({},{}),{}'.format(current_key[0],44                                  current_key[1],45                                  total_sum,46                                  )47              )48if __name__ == '__main__':...

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