6035193017

Committed 31 Aug 2023 08:55AM UTC coverage: 59.223%. Remained the same

Build # 6035193017

Build Type

push

github-actions

Committed by

web-flow

Commit Message

Update CODEOWNERS (#235)

* Update CODEOWNERS
---------

Co-authored-by: Vincent Janvid <69356202+Vince-janv@users.noreply.github.com>
Co-authored-by: Vincent Janvid <vincent.janvid@scilifelab.se>

Run Details

1021 of 1724 relevant lines covered (59.22%)

0.59 hits per line

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19.35

/statina/crud/find/plots/coverage_plot_data.py

from typing import Dict, List

from statina.models.database import DataBaseSample
from statina.models.server.plots.coverage import CoveragePlotSampleData
from statina.models.server.sample import SampleValidator, SampleWarning


def get_scatter_data_for_coverage_plot(
    samples: List[SampleValidator],
) -> Dict["str", CoveragePlotSampleData]:
    """Coverage Ratio data for Coverage Plot.
    Only adding samples with a zscore war
    ning"""

    data = {}
    for sample in samples:
        sample_warnings: SampleWarning = sample.warnings
        zscore_warnings = [
            sample_warnings.z_score_13,
            sample_warnings.z_score_18,
            sample_warnings.z_score_21,
        ]
        if set(zscore_warnings) == {"default"}:
            continue

        x = []
        y = []
        for chromosome in range(1, 23):
            ratio = sample.dict().get(f"Chr{chromosome}_Ratio")
            if ratio is None:
                continue
            y.append(ratio)
            x.append(chromosome)
        data[sample.sample_id] = CoveragePlotSampleData(x_axis=x, y_axis=y)
    return data


def get_box_data_for_coverage_plot(
    validated_samples: List[DataBaseSample],
) -> Dict[int, List[float]]:
    """Coverage Ratio data for Coverage Plot."""

    box_data = {}
    for chromosome in range(1, 23):
        box_data[chromosome] = []
        for sample in validated_samples:
            ratio = sample.dict().get(f"Chr{chromosome}_Ratio")
            if ratio is None:
                continue
            box_data[chromosome].append(ratio)
    return box_data

1	from typing import Dict, List	1✔
2
3	from statina.models.database import DataBaseSample	1✔
4	from statina.models.server.plots.coverage import CoveragePlotSampleData	1✔
5	from statina.models.server.sample import SampleValidator, SampleWarning	1✔
6
7
8	def get_scatter_data_for_coverage_plot(	1✔
9	samples: List[SampleValidator],
10	) -> Dict["str", CoveragePlotSampleData]:
11	"""Coverage Ratio data for Coverage Plot.
12	Only adding samples with a zscore war
13	ning"""
14
15	data = {}	×
16	for sample in samples:	×
17	sample_warnings: SampleWarning = sample.warnings	×
18	zscore_warnings = [	×
19	sample_warnings.z_score_13,
20	sample_warnings.z_score_18,
21	sample_warnings.z_score_21,
22	]
23	if set(zscore_warnings) == {"default"}:	×
24	continue	×
25
26	x = []	×
27	y = []	×
28	for chromosome in range(1, 23):	×
29	ratio = sample.dict().get(f"Chr{chromosome}_Ratio")	×
30	if ratio is None:	×
31	continue	×
32	y.append(ratio)	×
33	x.append(chromosome)	×
34	data[sample.sample_id] = CoveragePlotSampleData(x_axis=x, y_axis=y)	×
35	return data	×
36
37
38	def get_box_data_for_coverage_plot(	1✔
39	validated_samples: List[DataBaseSample],
40	) -> Dict[int, List[float]]:
41	"""Coverage Ratio data for Coverage Plot."""
42
43	box_data = {}	×
44	for chromosome in range(1, 23):	×
45	box_data[chromosome] = []	×
46	for sample in validated_samples:	×
47	ratio = sample.dict().get(f"Chr{chromosome}_Ratio")	×
48	if ratio is None:	×
49	continue	×
50	box_data[chromosome].append(ratio)	×
51	return box_data	×

Clinical-Genomics / statina / 6035193017

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