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Fix multiple analyses with the same reference genome #143

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Merged
tcezard merged 1 commit into from
Feb 5, 2026
Merged

Fix multiple analyses with the same reference genome #143

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4 changes: 2 additions & 2 deletions eva_sub_cli/executables/check_fasta_insdc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -132,11 +132,11 @@ def get_analyses_and_reference_genome_from_metadata(vcf_files_for_fasta, json_fi
else:
all_analyses.add(analysis_aliases[0])
# Get (single) assembly associated with these analyses
assemblies = [metadata.get_reference_assembly_for_analysis(analysis) for analysis in all_analyses]
assemblies = {metadata.get_reference_assembly_for_analysis(analysis) for analysis in all_analyses}
if len(assemblies) != 1:
logger.error(f'Could not determine assembly accession to check against fasta file, out of: {assemblies}')
return all_analyses, None
return all_analyses, assemblies[0]
return all_analyses, assemblies.pop()


def check_assembly_in_metadata(assembly_in_metadata):
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16 changes: 16 additions & 0 deletions tests/test_check_fasta_insdc.py
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Expand Up @@ -23,6 +23,22 @@ def test_get_analysis_and_reference_genome_from_metadata(self):
assert analyses == {'VD1'}
assert reference == 'GCA_000001405.27'

def test_get_analysis_and_reference_genome_from_metadata_multiple_analyses(self):
"""Test that multiple analyses with the same referenceGenome return that single assembly."""
working_dir = os.path.join(self.resource_dir, 'sample_checker')
metadata_json = os.path.join(working_dir, 'metadata.json')
vcf_file1 = os.path.join(working_dir, 'example1.vcf.gz') # VD1
vcf_file2 = os.path.join(working_dir, 'example2.vcf') # VD2
vcf_file3 = os.path.join(working_dir, 'example3.vcf') # VD3
os.chdir(working_dir)

# Multiple VCF files from different analyses, all with same referenceGenome
analyses, reference = get_analyses_and_reference_genome_from_metadata(
[vcf_file1, vcf_file2, vcf_file3], metadata_json
)
assert analyses == {'VD1', 'VD2', 'VD3'}
assert reference == 'GCA_000001405.27'

def test_get_analysis_and_reference_genome_from_metadata_absolute_paths(self):
working_dir = os.path.join(self.resource_dir, 'sample_checker')
metadata_json = os.path.join(working_dir, 'metadata.json')
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