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EVA-3323 Count remapped variants from logs only if remapping was done #7

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merged 3 commits into from
Sep 26, 2023
Merged

EVA-3323 Count remapped variants from logs only if remapping was done #7

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1003a47
only count remapped variants if remapping was required
nitin-ebi Sep 25, 2023
28bc633
update review comment
nitin-ebi Sep 25, 2023
438e75b
removing unused parameter
nitin-ebi Sep 25, 2023
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8 changes: 6 additions & 2 deletions eva_assembly_ingestion/assembly_ingestion_job.py
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Original file line number Diff line number Diff line change
Expand Up @@ -171,6 +171,7 @@ def process_one_assembly(self, source_assembly, instance, resume):

remapping_log = os.path.join(assembly_directory, 'remapping_process.log')
remap_cluster_config_file = os.path.join(assembly_directory, 'remap_cluster_config.yaml')
remapping_required = self.check_remapping_required(source_assembly)
remap_cluster_config = {
'taxonomy_id': self.taxonomy,
'source_assembly_accession': source_assembly,
Expand All @@ -183,7 +184,7 @@ def process_one_assembly(self, source_assembly, instance, resume):
'clustering_properties': clustering_template_file,
'clustering_instance': instance,
'remapping_config': cfg.config_file,
'remapping_required': self.check_remapping_required(source_assembly)
'remapping_required': remapping_required
}

for part in ['executable', 'nextflow', 'jar']:
Expand All @@ -210,7 +211,10 @@ def process_one_assembly(self, source_assembly, instance, resume):
finally:
os.chdir(curr_working_dir)
self.set_status_end(source_assembly)
self.count_variants_from_logs(assembly_directory, source_assembly)
if remapping_required:
self.count_variants_from_logs(assembly_directory, source_assembly, remapping_required)
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Suggested change
self.count_variants_from_logs(assembly_directory, source_assembly, remapping_required)
self.count_variants_from_logs(assembly_directory, source_assembly)

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corrected

else:
self.info(f"No remapping required. Skipping variant counts from logs")

def check_remapping_required(self, source_assembly):
return source_assembly != self.target_assembly
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