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@holtgrewe
holtgrewe committed Sep 22, 2023
1 parent a914a29 commit beb9c99
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Showing 9 changed files with 15,422 additions and 330 deletions.
82 changes: 41 additions & 41 deletions cases_qc/io/dragen.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@

from cases_qc import models
from cases_qc.io.utils import try_cast
import cases_qc.models.dragen
import cases_qc.models.dragen as models_dragen


def load_metrics_generic(
Expand All @@ -26,7 +26,7 @@ def load_metrics_generic(
metrics = []
for record in reader:
metrics.append(
models.DragenStyleMetric(
models_dragen.DragenStyleMetric(
section=record.get("section"),
entry=try_cast(record["entry"], (str, None)),
name=record.get("name"),
Expand All @@ -50,7 +50,7 @@ def load_metrics_generic(

def load_fragment_length_hist(
*, sample: str, input_file: typing.TextIO, caseqc: models.CaseQc
) -> cases_qc.models.dragen.DragenFragmentLengthHistogram:
) -> models_dragen.DragenFragmentLengthHistogram:
# skip first line
input_file.readline()

Expand All @@ -62,7 +62,7 @@ def load_fragment_length_hist(
keys.append(int(record["FragmentLength"]))
values.append(int(record["Count"]))

return models.DragenFragmentLengthHistogram.objects.create(
return models_dragen.DragenFragmentLengthHistogram.objects.create(
caseqc=caseqc,
sample=sample,
keys=keys,
Expand Down Expand Up @@ -101,134 +101,134 @@ def load_fine_hist_generic(

def load_wgs_fine_hist(
*, sample: str, input_file: typing.TextIO, caseqc: models.CaseQc
) -> cases_qc.models.dragen.DragenWgsFineHist:
) -> models_dragen.DragenWgsFineHist:
return load_fine_hist_generic(
sample=sample, input_file=input_file, caseqc=caseqc, model=models.DragenWgsFineHist
sample=sample, input_file=input_file, caseqc=caseqc, model=models_dragen.DragenWgsFineHist
)


def load_vc_hethom_ratio_metrics(
*, input_file: typing.TextIO, caseqc: models.CaseQc
) -> cases_qc.models.dragen.DragenVcHethomRatioMetrics:
) -> models_dragen.DragenVcHethomRatioMetrics:
"""Load contig het./hom. metrics from ``input_file`` into ``caseqc``"""
return load_metrics_generic(
input_file=input_file,
caseqc=caseqc,
model=models.DragenVcHethomRatioMetrics,
model=models_dragen.DragenVcHethomRatioMetrics,
)


def load_cnv_metrics(
*, input_file: typing.TextIO, caseqc: models.CaseQc
) -> cases_qc.models.dragen.DragenCnvMetrics:
) -> models_dragen.DragenCnvMetrics:
"""Load CNV metrics from ``input_file`` into ``caseqc``"""
return load_metrics_generic(
input_file=input_file,
caseqc=caseqc,
model=models.DragenCnvMetrics,
model=models_dragen.DragenCnvMetrics,
)


def load_mapping_metrics(
*, sample: str, input_file: typing.TextIO, caseqc: models.CaseQc
) -> cases_qc.models.dragen.DragenMappingMetrics:
) -> models_dragen.DragenMappingMetrics:
"""Load mapping metrics from ``input_file`` into ``caseqc``"""
return load_metrics_generic(
sample=sample,
input_file=input_file,
caseqc=caseqc,
model=models.DragenMappingMetrics,
model=models_dragen.DragenMappingMetrics,
)


def load_ploidy_estimation_metrics(
*, sample: str, input_file: typing.TextIO, caseqc: models.CaseQc
) -> cases_qc.models.dragen.DragenPloidyEstimationMetrics:
) -> models_dragen.DragenPloidyEstimationMetrics:
"""Load ploidy estimation metrics from ``input_file`` into ``caseqc``"""
return load_metrics_generic(
sample=sample,
input_file=input_file,
caseqc=caseqc,
model=models.DragenPloidyEstimationMetrics,
model=models_dragen.DragenPloidyEstimationMetrics,
)


def load_roh_metrics(
*, sample: str, input_file: typing.TextIO, caseqc: models.CaseQc
) -> cases_qc.models.dragen.DragenRohMetrics:
) -> models_dragen.DragenRohMetrics:
"""Load ROH metrics from ``input_file`` into ``caseqc``"""
return load_metrics_generic(
sample=sample,
input_file=input_file,
caseqc=caseqc,
model=models.DragenRohMetrics,
model=models_dragen.DragenRohMetrics,
)


def load_sv_metrics(
*, input_file: typing.TextIO, caseqc: models.CaseQc
) -> cases_qc.models.dragen.DragenSvMetrics:
) -> models_dragen.DragenSvMetrics:
"""Load SV calling metrics from ``input_file`` into ``caseqc``"""
return load_metrics_generic(
input_file=input_file,
caseqc=caseqc,
model=models.DragenSvMetrics,
model=models_dragen.DragenSvMetrics,
)


def load_time_metrics(
*, sample: str, input_file: typing.TextIO, caseqc: models.CaseQc
) -> cases_qc.models.dragen.DragenTimeMetrics:
) -> models_dragen.DragenTimeMetrics:
"""Load time metrics from ``input_file`` into ``caseqc``"""
return load_metrics_generic(
sample=sample,
input_file=input_file,
caseqc=caseqc,
model=models.DragenTimeMetrics,
model=models_dragen.DragenTimeMetrics,
)


def load_trimmer_metrics(
*, sample: str, input_file: typing.TextIO, caseqc: models.CaseQc
) -> cases_qc.models.dragen.DragenTrimmerMetrics:
) -> models_dragen.DragenTrimmerMetrics:
"""Load time metrics from ``input_file`` into ``caseqc``"""
return load_metrics_generic(
sample=sample,
input_file=input_file,
caseqc=caseqc,
model=models.DragenTrimmerMetrics,
model=models_dragen.DragenTrimmerMetrics,
)


def load_vc_metrics(
*, input_file: typing.TextIO, caseqc: models.CaseQc
) -> cases_qc.models.dragen.DragenTrimmerMetrics:
) -> models_dragen.DragenTrimmerMetrics:
"""Load variant caller metrics from ``input_file`` into ``caseqc``"""
return load_metrics_generic(
input_file=input_file,
caseqc=caseqc,
model=models.DragenVcMetrics,
model=models_dragen.DragenVcMetrics,
)


def load_wgs_contig_mean_cov(
*, sample: str, input_file: typing.TextIO, caseqc: models.CaseQc
) -> cases_qc.models.dragen.DragenWgsContigMeanCovMetrics:
) -> models_dragen.DragenWgsContigMeanCovMetrics:
"""Load time metrics from ``input_file`` into ``caseqc``"""
fieldnames = ("contig_name", "contig_len", "cov")
reader = csv.DictReader(f=input_file, fieldnames=fieldnames, delimiter=",")

metrics = []
for record in reader:
metrics.append(
models.DragenStyleCoverage(
models_dragen.DragenStyleCoverage(
contig_name=record["contig_name"],
contig_len=int(record["contig_len"]),
cov=float(record["cov"]),
)
)

return models.DragenWgsContigMeanCovMetrics.objects.create(
return models_dragen.DragenWgsContigMeanCovMetrics.objects.create(
caseqc=caseqc,
sample=sample,
metrics=metrics,
Expand All @@ -237,19 +237,19 @@ def load_wgs_contig_mean_cov(

def load_wgs_coverage_metrics(
*, sample: str, input_file: typing.TextIO, caseqc: models.CaseQc
) -> cases_qc.models.dragen.DragenWgsCoverageMetrics:
) -> models_dragen.DragenWgsCoverageMetrics:
"""Load time metrics from ``input_file`` into ``caseqc``"""
return load_metrics_generic(
sample=sample,
input_file=input_file,
caseqc=caseqc,
model=models.DragenWgsCoverageMetrics,
model=models_dragen.DragenWgsCoverageMetrics,
)


def load_wgs_hist(
*, sample: str, input_file: typing.TextIO, caseqc: models.CaseQc
) -> cases_qc.models.dragen.DragenWgsHist:
) -> models_dragen.DragenWgsHist:
"""Load WGS histogram metrics from ``input_file`` into ``caseqc``."""
fieldnames = ("key", "value")
reader = csv.DictReader(f=input_file, fieldnames=fieldnames, delimiter=",")
Expand All @@ -260,7 +260,7 @@ def load_wgs_hist(
keys.append(record["key"])
values.append(float(record["value"]))

return models.DragenWgsHist.objects.create(
return models_dragen.DragenWgsHist.objects.create(
caseqc=caseqc,
sample=sample,
keys=keys,
Expand All @@ -270,65 +270,65 @@ def load_wgs_hist(

def load_wgs_overall_mean_cov(
*, sample: str, input_file: typing.TextIO, caseqc: models.CaseQc
) -> cases_qc.models.dragen.DragenWgsOverallMeanCov:
) -> models_dragen.DragenWgsOverallMeanCov:
"""Load overall mean coverage metrics from ``input_file`` into ``caseqc``"""
return load_metrics_generic(
sample=sample,
input_file=input_file,
caseqc=caseqc,
model=models.DragenWgsOverallMeanCov,
model=models_dragen.DragenWgsOverallMeanCov,
fieldnames=("entry", "value"),
)


def load_region_coverage_metrics(
*, sample: str, region_name: str, input_file: typing.TextIO, caseqc: models.CaseQc
) -> cases_qc.models.dragen.DragenRegionCoverageMetrics:
) -> models_dragen.DragenRegionCoverageMetrics:
"""Load region coverage metrics from ``input_file`` into ``caseqc``"""
return load_metrics_generic(
sample=sample,
region_name=region_name,
input_file=input_file,
caseqc=caseqc,
model=models.DragenRegionCoverageMetrics,
model=models_dragen.DragenRegionCoverageMetrics,
)


def load_region_fine_hist(
*, sample: str, region_name: str, input_file: typing.TextIO, caseqc: models.CaseQc
) -> cases_qc.models.dragen.DragenRegionFineHist:
) -> models_dragen.DragenRegionFineHist:
"""Load region fine histogram from ``input_file`` into ``caseqc``"""
return load_fine_hist_generic(
sample=sample,
region_name=region_name,
input_file=input_file,
caseqc=caseqc,
model=models.DragenRegionFineHist,
model=models_dragen.DragenRegionFineHist,
)


def load_region_hist(
*, sample: str, region_name: str, input_file: typing.TextIO, caseqc: models.CaseQc
) -> cases_qc.models.dragen.DragenRegionHist:
) -> models_dragen.DragenRegionHist:
"""Load region histogram from ``input_file`` into ``caseqc``"""
return load_metrics_generic(
sample=sample,
region_name=region_name,
input_file=input_file,
caseqc=caseqc,
model=models.DragenRegionHist,
model=models_dragen.DragenRegionHist,
fieldnames=("entry", "value"),
)


def load_region_overall_mean_cov(
*, sample: str, region_name: str, input_file: typing.TextIO, caseqc: models.CaseQc
) -> cases_qc.models.dragen.DragenRegionOverallMeanCov:
) -> models_dragen.DragenRegionOverallMeanCov:
"""Load region histogram from ``input_file`` into ``caseqc``"""
return load_metrics_generic(
sample=sample,
region_name=region_name,
input_file=input_file,
caseqc=caseqc,
model=cases_qc.models.dragen.DragenRegionOverallMeanCov,
model=models_dragen.DragenRegionOverallMeanCov,
)
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