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| author | Lan Hui <lanhui@zjnu.edu.cn> | 2025-04-16 15:33:50 +0800 |
|---|---|---|
| committer | Lan Hui <lanhui@zjnu.edu.cn> | 2025-04-16 15:33:50 +0800 |
| commit | 52a1fc0d30cd48c822ca3b0bde5a4cd5f7ed2ac2 (patch) | |
| tree | 041a25f01b8bdb63979076550dc0ef2fd6104092 /Code | |
| parent | ada33aee714635628d9bdab3cba9f3ec3f2f92a4 (diff) | |
Fix key errors
Diffstat (limited to 'Code')
| -rw-r--r-- | Code/parse_ena_xml.py | 8 |
1 files changed, 4 insertions, 4 deletions
diff --git a/Code/parse_ena_xml.py b/Code/parse_ena_xml.py index 7122a73..c9faefe 100644 --- a/Code/parse_ena_xml.py +++ b/Code/parse_ena_xml.py @@ -199,7 +199,7 @@ def get_singular_form(w): return w -def get_tissue(run_id, d_run, sample_id, d_sample, experiment_id, d_experiment, study_id, d_study): +def get_tissue(run_id, d_run, experiment_id, d_experiment, sample_id, d_sample, study_id, d_study): ''' Extract tissue name from s. s may contain several tissue names, return them ordered by frequency. ''' tissue = '' @@ -313,13 +313,13 @@ if __name__ == '__main__': json_dict = {} for k in sorted(d_run_keys): d = {} - k2 = d_experiment[k2]['sample_id'] - k3 = d_run[k]['experiment_id'] + k2 = d_run[k]['experiment_id'] + k3 = d_experiment[k2]['sample_id'] if k2 in d_experiment else 'SAM_UNKNOWN' k4 = d_experiment[k2]['study_id'] if k2 in d_experiment else 'PRJ_UNKNOWN' d['tissue'] = d['library_strategy'] = d['library_source'] = d['sample_id'] = '.' if k2 in d_experiment: d['sample_id'] = d_experiment[k2]['sample_id'] - d['tissue'] = get_tissue(k, d_run, k2, d_sample, k3, d_experiment, k4, d_study) + d['tissue'] = get_tissue(k, d_run, k2, d_experiment, k3, d_sample, k4, d_study) d['library_strategy'] = d_experiment[k2]['library_strategy'] d['library_source'] = d_experiment[k2]['library_source'] d['detail'] = 'TBA' |