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Move call of sketchlibAssemblyQC in query assign #317

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merged 2 commits into from
Jul 9, 2024
Merged

Move call of sketchlibAssemblyQC in query assign #317

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6ec390f
feat: move sketchlibAssemblyQC call in assign
absternator Jul 5, 2024
3ee8639
chore: update PopPUNK version to 2.6.7
absternator Jul 5, 2024
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2 changes: 1 addition & 1 deletion PopPUNK/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@

'''PopPUNK (POPulation Partitioning Using Nucleotide Kmers)'''

__version__ = '2.6.6'
__version__ = '2.6.7'

# Minimum sketchlib version
SKETCHLIB_MAJOR = 2
Expand Down
49 changes: 26 additions & 23 deletions PopPUNK/assign.py
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Original file line number Diff line number Diff line change
Expand Up @@ -265,8 +265,6 @@ def assign_query(dbFuncs,
deviceid,
save_partial_query_graph):
"""Code for assign query mode for CLI"""
from .qc import sketchlibAssemblyQC

createDatabaseDir = dbFuncs['createDatabaseDir']
constructDatabase = dbFuncs['constructDatabase']
readDBParams = dbFuncs['readDBParams']
Expand All @@ -292,18 +290,6 @@ def assign_query(dbFuncs,
use_gpu = gpu_sketch,
deviceid = deviceid)

if qc_dict["run_qc"]:
pass_assembly_qc, fail_assembly_qc = \
sketchlibAssemblyQC(output,
qNames,
qc_dict)
if len(fail_assembly_qc) > 0:
sys.stderr.write(f"{len(fail_assembly_qc)} samples failed:\n"
f"{','.join(fail_assembly_qc.keys())}\n")
qNames = [x for x in qNames if x in pass_assembly_qc]
if len(qNames) == 0:
sys.exit(1)

isolateClustering = assign_query_hdf5(dbFuncs,
ref_db,
qNames,
Expand Down Expand Up @@ -367,7 +353,7 @@ def assign_query_hdf5(dbFuncs,
from .network import get_vertex_list
from .network import printExternalClusters
from .network import vertex_betweenness

from .qc import sketchlibAssemblyQC

from .plot import writeClusterCsv

Expand All @@ -380,6 +366,23 @@ def assign_query_hdf5(dbFuncs,
from .utils import readPickle
from .utils import update_distance_matrices
from .utils import createOverallLineage

failed_assembly_qc = {}
failed_assembly_samples = frozenset()
if qc_dict["run_qc"]:
pass_assembly_qc, failed_assembly_qc = \
sketchlibAssemblyQC(output,
qNames,
qc_dict)
failed_assembly_samples = frozenset(failed_assembly_qc.keys())
if len(failed_assembly_qc) > 0:
sys.stderr.write(f"{len(failed_assembly_qc)} samples failed:\n"
f"{','.join(failed_assembly_samples)}\n")

qNames = [x for x in qNames if x in pass_assembly_qc]
if len(qNames) == 0:
write_qc_failure_report(failed_assembly_samples, [failed_assembly_qc], output)
sys.exit(1)

joinDBs = dbFuncs['joinDBs']
queryDatabase = dbFuncs['queryDatabase']
Expand Down Expand Up @@ -489,18 +492,18 @@ def assign_query_hdf5(dbFuncs,
# QC distance matrix
if qc_dict['run_qc']:
sys.stderr.write("Running QC on distance matrix\n")
seq_names_passing, failed_samples_dict = qcDistMat(qrDistMat, rNames, qNames, ref_db, qc_dict)
failed_samples = frozenset(qNames) - frozenset(seq_names_passing)
if len(failed_samples) > 0:
sys.stderr.write(f"{len(failed_samples)} samples failed:\n"
f"{','.join(failed_samples)}\n")
write_qc_failure_report(failed_samples, [failed_samples_dict], output)
seq_names_passing, failed_distmatrix_qc = qcDistMat(qrDistMat, rNames, qNames, ref_db, qc_dict)
failed_distmatrix_samples = frozenset(qNames) - frozenset(seq_names_passing)
if len(failed_distmatrix_samples) > 0:
sys.stderr.write(f"{len(failed_distmatrix_samples)} samples failed:\n"
f"{','.join(failed_distmatrix_samples)}\n")
write_qc_failure_report(failed_distmatrix_samples | failed_assembly_samples, [failed_distmatrix_qc, failed_assembly_qc], output)

if len(failed_samples) == len(qNames):
if len(failed_distmatrix_samples) == len(qNames):
sys.exit(1)
else:
qNames, qrDistMat = \
prune_query_distance_matrix(rNames, qNames, failed_samples, qrDistMat)[0:2]
prune_query_distance_matrix(rNames, qNames, failed_distmatrix_samples, qrDistMat)[0:2]

# Load the network based on supplied options (never used for lineage models)
if model.type != 'lineage':
Expand Down
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