diff extract_tables.py @ 25:758e5bc32bbb draft

Uploaded

--- a/extract_tables.py	Mon Nov 16 14:24:59 2020 +0000
+++ b/extract_tables.py	Thu Nov 19 10:21:04 2020 +0000
@@ -1,62 +1,91 @@
 import argparse
 import json
-import os
 import pathlib
-
 from datetime import datetime
 
+FILE_FORMAT = 'fastq'
+
 parser = argparse.ArgumentParser()
-parser.add_argument('--studies',dest='studies_json_path', required=True)
-parser.add_argument('--out_dir',dest='out_path', required=True)
+parser.add_argument('--studies', dest='studies_json_path', required=True)
+parser.add_argument('--out_dir', dest='out_path', required=True)
+parser.add_argument('--action', dest='action', required=True)
 args = parser.parse_args()
 
-
-with open(args.studies_json_path,'r') as studies_json_file:
+with open(args.studies_json_path, 'r') as studies_json_file:
     studies_dict = json.load(studies_json_file)
-
 studies_table = open(pathlib.Path(args.out_path) / 'studies.tsv', 'w')
-studies_table.write('\t'.join(['alias','status','accession','title','study_type','study_abstract','pubmed_id','submission_date']) + '\n')
-
+studies_table.write('\t'.join(['alias', 'status', 'accession', 'title', 'study_type',
+                               'study_abstract', 'pubmed_id', 'submission_date']) + '\n')
 samples_table = open(pathlib.Path(args.out_path) / 'samples.tsv', 'w')
+experiments_table = open(pathlib.Path(args.out_path) / 'experiments.tsv', 'w')
+experiments_table.write('\t'.join(['alias', 'status', 'accession', 'title', 'study_alias',
+                                   'sample_alias', 'design_description', 'library_name',
+                                   'library_strategy', 'library_source', 'library_selection',
+                                   'library_layout', 'insert_size',
+                                   'library_construction_protocol', 'platform', 'instrument_model',
+                                   'submission_date']) + '\n')
+runs_table = open(pathlib.Path(args.out_path) / 'runs.tsv', 'w')
+runs_table.write('\t'.join(['alias', 'status', 'accession', 'experiment_alias', 'file_name',
+                            'file_format', 'file_checksum', 'submission_date']) + '\n')
 
-experiments_table = open(pathlib.Path(args.out_path) / 'experiments.tsv', 'w')
-experiments_table.write('\t'.join(['alias','status','accession','title','study_alias','sample_alias','design_description','library_name','library_strategy','library_source','library_selection','library_layout','insert_size','library_construction_protocol','platform','instrument_model','submission_date'])+ '\n')
-
-runs_table = open(pathlib.Path(args.out_path) / 'runs.tsv', 'w')
-runs_table.write('\t'.join(['alias','status','accession','experiment_alias','file_name','file_format','file_checksum','submission_date'])+ '\n')
-
-action = 'add'
-viral_submission = False
+action = args.action
 
 dt_oobj = datetime.now(tz=None)
 timestamp = dt_oobj.strftime("%Y%m%d_%H:%M:%S")
 for study_index, study in enumerate(studies_dict):
-    study_alias = 'study_'+str(study_index)+'_'+timestamp
-    studies_table.write('\t'.join([study_alias,action,'ENA_accession',study['title'], study['type'],study['abstract'],study['pubmed_id'],'ENA_submission_data']))
-    if "geo_location" in study['samples'][0].keys(): # sample belongs to a viral sample
-        samples_table.write('\t'.join(['alias','status','accession','title','scientific_name','taxon_id','sample_description','collection_date','geographic_location','host_common_name','host_subject_id','host_health_state','host_sex','host_scientific_name','collector_name','collecting_institution','isolate','submission_date']) + '\n')
+    study_alias = 'study_' + str(study_index) + '_' + timestamp
+    studies_table.write('\t'.join([study_alias, action, 'ENA_accession', study['title'],
+                                   study['type'], study['abstract'], study['pubmed_id'],
+                                   'ENA_submission_data']))
+    if "geo_location" in study['samples'][0].keys():           # sample belongs to a viral sample
+        samples_table.write('\t'.join(['alias', 'status', 'accession', 'title', 'scientific_name',
+                                       'taxon_id', 'sample_description', 'collection_date',
+                                       'geographic_location', 'host_common_name', 'host_subject_id',
+                                       'host_health_state', 'host_sex', 'host_scientific_name',
+                                       'collector_name', 'collecting_institution', 'isolate',
+                                       'submission_date']) + '\n')
     else:
-        samples_table.write('\t'.join(['alias','status','accession','title','scientific_name','taxon_id','sample_description','submission_date']) + '\n')
-    for sample_index,sample in enumerate(study['samples']):
-        sample_alias = 'sample_'+str(sample_index)+'_'+timestamp
-        if "geo_location" in sample.keys(): # sample belongs to a viral sample
+        samples_table.write('\t'.join(['alias', 'status', 'accession', 'title', 'scientific_name',
+                                       'taxon_id', 'sample_description', 'submission_date']) + '\n')
+    for sample_index, sample in enumerate(study['samples']):
+        sample_alias = 'sample_' + str(sample_index) + '_' + timestamp
+        if "geo_location" in sample.keys():  # sample belongs to a viral sample
             if sample['collector_name'] == '':
                 sample['collector_name'] = 'unknown'
-            samples_table.write('\t'.join([sample_alias,action,'ena_accession',sample['title'],sample['tax_name'], sample['tax_id'],sample['description'],sample['collection_date'],sample['geo_location'],sample['host_common_name'],sample['host_subject_id'],sample['host_health_state'],sample['host_sex'],sample['host_scientific_name'],sample['collector_name'],sample['collecting_institution'],sample['isolate'],'ENA_submission_date'])+ '\n')
+            samples_table.write('\t'.join([sample_alias, action, 'ena_accession', sample['title'],
+                                           sample['tax_name'], sample['tax_id'],
+                                           sample['description'], sample['collection_date'],
+                                           sample['geo_location'], sample['host_common_name'],
+                                           sample['host_subject_id'], sample['host_health_state'],
+                                           sample['host_sex'], sample['host_scientific_name'],
+                                           sample['collector_name'],
+                                           sample['collecting_institution'], sample['isolate'],
+                                           'ENA_submission_date']) + '\n')
         else:
-            samples_table.write('\t'.join([sample_alias,action,'ena_accession',sample['title'],sample['tax_name'], sample['tax_id'],sample['description'],'ENA_submission_date'])+ '\n')
-        for exp_index,exp in enumerate(sample['experiments']):
-            exp_alias = 'experiment_'+str(exp_index)+'.'+str(sample_index)+'_'+timestamp
-            lib_alias = 'library_'+str(exp_index)+'_'+str(sample_index)
-            experiments_table.write('\t'.join([exp_alias,action,'accession_ena',exp['title'],study_alias,sample_alias,exp['experiment_design'],lib_alias,exp['library_strategy'],exp['library_source'],exp['library_selection'],exp['library_layout'].lower(),exp['insert_size'],exp['library_construction_protocol'],exp['platform'],exp['instrument_model'],'submission_date_ENA']) + '\n')
+            samples_table.write('\t'.join([sample_alias, action, 'ena_accession', sample['title'],
+                                           sample['tax_name'], sample['tax_id'],
+                                           sample['description'], 'ENA_submission_date']) + '\n')
+        for exp_index, exp in enumerate(sample['experiments']):
+            exp_alias = 'experiment_' + str(exp_index) + '.' + str(sample_index) + '_' + timestamp
+            lib_alias = 'library_' + str(exp_index) + '_' + str(sample_index)
+            experiments_table.write('\t'.join([exp_alias, action, 'accession_ena', exp['title'],
+                                               study_alias, sample_alias, exp['experiment_design'],
+                                               lib_alias, exp['library_strategy'],
+                                               exp['library_source'], exp['library_selection'],
+                                               exp['library_layout'].lower(), exp['insert_size'],
+                                               exp['library_construction_protocol'],
+                                               exp['platform'], exp['instrument_model'],
+                                               'submission_date_ENA']) + '\n')
             run_index = 0
             # exp['runs'] is a list of lists
             for run in exp['runs']:
                 run_index += 1
-                run_alias = '.'.join(['run_'+str(run_index),str(exp_index),str(sample_index)]) + '_' +timestamp
+                run_alias = '.'.join(['run_' + str(run_index), str(exp_index), str(sample_index)]) \
+                            + '_' + timestamp
                 for file_entry in run:
-                    file_format = 'fastq'
-                    runs_table.write('\t'.join([run_alias,action,'ena_run_accession',exp_alias,file_entry,file_format,'file_checksum','submission_date_ENA']) + '\n')
+                    runs_table.write('\t'.join([run_alias, action, 'ena_run_accession', exp_alias,
+                                                file_entry, FILE_FORMAT, 'file_checksum',
+                                                'submission_date_ENA']) + '\n')
 
 studies_table.close()
 samples_table.close()