diff extract_tables.py @ 15:d85e35a36715 draft

Uploaded

--- a/extract_tables.py	Tue Sep 22 20:36:41 2020 +0000
+++ b/extract_tables.py	Thu Sep 24 10:14:41 2020 +0000
@@ -16,7 +16,6 @@
 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')
-samples_table.write('\t'.join(['alias','status','accession','title','scientific_name','taxon_id','sample_description','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')
@@ -25,23 +24,33 @@
 runs_table.write('\t'.join(['alias','status','accession','experiment_alias','file_name','file_format','file_checksum','submission_date'])+ '\n')
 
 action = 'add'
+viral_submission = False
 for study_index, study in enumerate(studies_dict):
     study_alias = 'study_'+str(study_index)
     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)
-        samples_table.write('\t'.join([sample_alias,action,'ena_accession',sample['title'],sample['tax_name'], sample['tax_id'],sample['description'],'ENA_submission_date'])+ '\n')
+        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')
+        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)
             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'],exp['insert_size'],exp['library_construction_protocol'],exp['platform'],exp['instrument_model'],'submission_date_ENA']) + '\n')
+            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(exp_index),str(sample_index),str(run_index)])
                 for file_entry in run:
-                    file_format = 'fastq.gz' if os.path.splitext(file_entry)[-1] == '.gz' else 'fastq.bz2'
+                    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')
 
 studies_table.close()