diff --git a/seqr/management/tests/load_rna_seq_tests.py b/seqr/management/tests/load_rna_seq_tests.py index 6353809f5a..936967322a 100644 --- a/seqr/management/tests/load_rna_seq_tests.py +++ b/seqr/management/tests/load_rna_seq_tests.py @@ -68,9 +68,7 @@ def test_tpm(self, mock_utils_logger): 'NA19675_D2\t1kg project nåme with uniçøde\t\tENSG00000240361\t12.6\t\n', 'NA19675_D2\t1kg project nåme with uniçøde\t\tENSG00000233750\t1.26\t\n', 'NA19678_D1\t1kg project nåme with uniçøde\t\tENSG00000233750\t 6.04\twhole_blood\n', - 'GTEX-001\t1kg project nåme with uniçøde\t\tENSG00000240361\t3.1\tinvalid\n', 'NA19677\t1kg project nåme with uniçøde\t\tENSG00000233750\t5.31\tmuscle\n', - 'GTEX-001\t1kg project nåme with uniçøde\t\tENSG00000233750\t7.8\tmuscle\n', 'NA19678\tTest Reprocessed Project\t\tENSG00000240361\t0.2\twhole_blood\n', ], unmatched_samples='NA19677, NA19678, NA19678_D1', diff --git a/seqr/views/apis/data_manager_api_tests.py b/seqr/views/apis/data_manager_api_tests.py index cbaf6fe977..5f6c6bbc9b 100644 --- a/seqr/views/apis/data_manager_api_tests.py +++ b/seqr/views/apis/data_manager_api_tests.py @@ -708,8 +708,6 @@ def test_kibana_proxy(self): ['NA19675_D2', '1kg project nåme with uniçøde', 'ENSG00000233750', 'NA19675_D2', 'muscle', 0.0], # no matched individual NA19675_D3 ['NA19675_D3', '1kg project nåme with uniçøde', 'ENSG00000233750', 'NA19675_D3', 'fibroblasts', 0.064], - # skip GTEX samples - ['GTEX_001', '1kg project nåme with uniçøde', 'ENSG00000233750', 'NA19675_D3', 'whole_blood', 1.95], # a different project sample NA20888 ['NA20888', 'Test Reprocessed Project', 'ENSG00000240361', 'NA20888', 'muscle', 0.112], # a project mismatched sample NA20878 diff --git a/seqr/views/utils/dataset_utils.py b/seqr/views/utils/dataset_utils.py index fdf1f4746b..2738652a76 100644 --- a/seqr/views/utils/dataset_utils.py +++ b/seqr/views/utils/dataset_utils.py @@ -294,7 +294,7 @@ def _add_splice_rank(sample_data_rows): 'tpm': { 'model_class': RnaSeqTpm, 'columns': TPM_HEADER_COLS, - 'additional_kwargs': {'should_skip': lambda row: row[SAMPLE_ID_COL].startswith('GTEX')}, + 'additional_kwargs': {}, }, 'splice_outlier': { 'model_class': RnaSeqSpliceOutlier, @@ -331,7 +331,7 @@ def _validate_rna_header(header, column_map): def _load_rna_seq_file( file_path, user, potential_loaded_samples, update_sample_models, save_sample_data, get_matched_sample, column_map, mapping_file=None, allow_missing_gene=False, ignore_extra_samples=False, - should_skip=None, format_fields=None, + format_fields=None, ): sample_id_to_individual_id_mapping = {} @@ -349,8 +349,6 @@ def _load_rna_seq_file( gene_ids = set() for line in tqdm(parsed_f, unit=' rows'): row = dict(zip(header, line)) - if should_skip and should_skip(row): - continue row_dict = {mapped_key: row[col] for mapped_key, col in column_map.items()} for mapped_key, format_func in (format_fields or {}).items():