diff --git a/src/encoded/audit/experiment.py b/src/encoded/audit/experiment.py index ad756e6dc2d..c1346396a6a 100644 --- a/src/encoded/audit/experiment.py +++ b/src/encoded/audit/experiment.py @@ -696,7 +696,7 @@ def check_experiment_dnase_seq_standards(experiment, link_to_standards): fastq_files = files_structure.get('fastq_files').values() alignment_files = files_structure.get('alignments').values() - signal_files = files_structure.get('signal_files').values() + signal_files = files_structure.get('normalized_signal_files').values() assay_term_name = experiment['assay_term_name'] pipeline_title = scanFilesForPipelineTitle_not_chipseq( @@ -849,7 +849,6 @@ def check_experiment_dnase_seq_standards(experiment, for f in metric['quality_metric_of']: file_names.append(f.split('/')[2]) file_list.append(f) - file_names_string = str(file_names).replace('\'', ' ') file_names_links = [audit_link(path_to_text(file), file) for file in file_list] detail = ('Replicate concordance in DNase-seq experiments is measured by ' 'calculating the Pearson correlation between signal quantification ' @@ -5208,6 +5207,7 @@ def create_files_mapping(files_list, excluded): 'transcript_quantifications_files': {}, 'microRNA_quantifications_files': {}, 'signal_files': {}, + 'normalized_signal_files': {}, 'preferred_default_idr_peaks': {}, 'idr_thresholded_peaks': {}, 'cpg_quantifications': {}, @@ -5272,6 +5272,9 @@ def create_files_mapping(files_list, excluded): if file_output and file_output == 'signal of unique reads': to_return['signal_files'][file_object['@id']] = file_object + if file_output and file_output == 'read-depth normalized signal': + to_return['normalized_signal_files'][file_object['@id']] = file_object + if file_output and file_output == 'optimal IDR thresholded peaks': to_return['preferred_default_idr_peaks'][ file_object['@id'] diff --git a/src/encoded/tests/test_audit_experiment.py b/src/encoded/tests/test_audit_experiment.py index 50ba12075d2..20d5f3dd685 100644 --- a/src/encoded/tests/test_audit_experiment.py +++ b/src/encoded/tests/test_audit_experiment.py @@ -2818,7 +2818,10 @@ def test_audit_experiment_dnase_low_correlation(testapp, analysis_step_version_bam, analysis_step_bam, pipeline_bam): - testapp.patch_json(bigWig_file['@id'], {'dataset': base_experiment['@id']}) + testapp.patch_json(bigWig_file['@id'], { + 'dataset': base_experiment['@id'], + 'output_type': 'read-depth normalized signal' + }) testapp.patch_json( correlation_quality_metric['@id'], {'quality_metric_of': [bigWig_file['@id']], 'Pearson correlation': 0.15})