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| -rw-r--r-- | Code/make_experiment_library_info_file.py | 22 |
1 files changed, 22 insertions, 0 deletions
diff --git a/Code/make_experiment_library_info_file.py b/Code/make_experiment_library_info_file.py new file mode 100644 index 0000000..9578945 --- /dev/null +++ b/Code/make_experiment_library_info_file.py @@ -0,0 +1,22 @@ +# Usage: python3 make_experiment_library_info_file.py +# +# Purpose: build a file (see EXPERIMENT_LIBRARY_INFO_FILE) that tells whether an experiment is RNA-seq. +# +# 2025-10-28, hui + +from configure import EXPERIMENT_LIBRARY_INFO_FILE, EXPERIMENT_INFO_DIR +from parse_ena_xml import parse_experiment +import glob, os + +result = [] +for fname in sorted(glob.glob(os.path.join(EXPERIMENT_INFO_DIR, '*'))): + _, experiment_id = os.path.split(fname) + d = parse_experiment(fname) + result.append([experiment_id, d[experiment_id]['library_strategy'], d[experiment_id]['library_source']]) + +print(f'Saving to {EXPERIMENT_LIBRARY_INFO_FILE}') +with open(EXPERIMENT_LIBRARY_INFO_FILE, 'a') as f: + for x in result: + f.write('\t'.join(x) + '\n') +print('Done. Saved %d lines.' % (len(result))) + |