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ENCD-5796 Update DNase audit to check for QC on correct file type #3777

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ENCD-5796 Update DNase audit to check for QC on correct file type #3777

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7 changes: 5 additions & 2 deletions src/encoded/audit/experiment.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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(
Expand Down Expand Up @@ -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 '
Expand Down Expand Up @@ -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': {},
Expand Down Expand Up @@ -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']
Expand Down
5 changes: 4 additions & 1 deletion src/encoded/tests/test_audit_experiment.py
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Expand Up @@ -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})
Expand Down