Mercurial > repos > ieguinoa > ena_upload
changeset 13:91a3a617d94b draft
Uploaded
| author | ieguinoa |
|---|---|
| date | Fri, 18 Sep 2020 14:29:47 +0000 |
| parents | 6694e2543e4b |
| children | 436da36c6114 |
| files | extract_tables.py |
| diffstat | 1 files changed, 2 insertions(+), 2 deletions(-) [+] |
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--- a/extract_tables.py Fri Sep 18 13:56:37 2020 +0000 +++ b/extract_tables.py Fri Sep 18 14:29:47 2020 +0000 @@ -34,14 +34,14 @@ 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()