comparison extract_tables.py @ 14:436da36c6114 draft

Uploaded

13:91a3a617d94b

        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')
        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'].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'
                    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()
experiments_table.close()

14:436da36c6114

        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')
        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')
            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'
                    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()
experiments_table.close()