Basic filtering system and tests completed
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This commit is contained in:
Harrison Deng 2023-06-26 17:20:40 +00:00
parent f2bdbaa0b0
commit 515d790844
11 changed files with 158 additions and 13 deletions

17
.vscode/settings.json vendored Normal file
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@ -0,0 +1,17 @@
{
"python.testing.pytestArgs": [],
"python.testing.unittestEnabled": false,
"python.testing.pytestEnabled": true,
"python.linting.pylintArgs": [
"--rcfile=setup.cfg"
],
"python.analysis.autoSearchPaths": true,
"python.analysis.extraPaths": [
"src"
],
"cSpell.words": [
"pytest",
"pyvcf",
"vcfs"
],
}

5
Jenkinsfile vendored
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@ -9,7 +9,6 @@ pipeline {
}
stage("unit tests") {
steps {
// TODO Update the
sh returnStatus: true, script: "python -m pytest --junitxml=unit_tests.xml --cov-report xml:test_coverage.xml --cov=program"
xunit checksName: '', tools: [JUnit(excludesPattern: '', pattern: 'test_results.xml', stopProcessingIfError: true)]
cobertura autoUpdateHealth: false, autoUpdateStability: false, coberturaReportFile: 'test_coverage.xml', failUnhealthy: false, failUnstable: false, maxNumberOfBuilds: 64, lineCoverageTargets: '50, 0, 0', methodCoverageTargets: '50, 0, 0', onlyStable: false, sourceEncoding: 'ASCII', zoomCoverageChart: false
@ -18,7 +17,7 @@ pipeline {
stage("build") {
steps {
sh "python -m build"
// Additional build steps go here
// TODO Additional build steps go here
}
}
stage("test installation") {
@ -30,7 +29,7 @@ pipeline {
stage("archive") {
steps {
archiveArtifacts artifacts: 'dist/*.tar.gz, dist/*.whl'
// Additional archival or documentation steps go here
// TODO Additional archival or documentation steps go here
}
}
stage("publish") {

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@ -8,3 +8,4 @@ dependencies:
- pytest
- twine
- sphinx
- pyvcf

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@ -1,17 +1,17 @@
[metadata]
name = sample
name = modvcfsamples
version = 0.0.1
[options]
package_dir =
= src
# install_requires =
# cachier ==2.1
= ./src
install_requires =
pyvcf ==0.6.8
# [options.entry_points]
# console_scripts =
# avariantas = program.program:entry_function
[options.entry_points]
console_scripts =
modvcfsamples = modvcfsamples.cli:main
[tool:pytest]
pythonpath = src

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@ -0,0 +1,3 @@
from setuptools import setup
setup()

39
src/modvcfsamples/cli.py Normal file
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import argparse
import os
from modvcfsamples import sample
def run(vcfs: list[str], only: list[str], output_dir: str):
for vcf in vcfs:
vcf_records = sample.get_records_from_vcf(vcf)
sample.filter_all_sample_datatypes(vcf_records, *only)
sample.write_records_to_vcf(vcf_records, os.path.join(output_dir, os.path.basename(vcf)))
def main():
parser = argparse.ArgumentParser()
parser.add_argument(
"vcfs",
help="The VCFs to run filtering on",
nargs="+",
metavar="I",
type=str
)
parser.add_argument(
"output_dir",
help="The output directory",
metavar="O",
type=str
)
parser.add_argument(
"--only",
"-n",
help="Remove everything but the sample datatype",
action="append",
type=str
)
args = parser.parse_args()
run(args.vcfs, args.only, args.output_dir)
if __name__ == "__main__":
main()

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@ -0,0 +1,34 @@
import vcf
from collections import namedtuple
from copy import deepcopy
def get_records_from_vcf(path: str):
vcf_records = []
with open(path, "r") as vcf_stream:
reader = vcf.Reader(vcf_stream)
for record in reader:
vcf_records.append(record)
return vcf_records
def filter_sample_datatype(record, *datatypes: str):
call_data = namedtuple("Data", *datatypes)
filtered_calls = []
modified_record = deepcopy(record)
for call in record.samples:
kept_data = {}
for datatype in datatypes:
kept_data[datatype] = call[datatype]
filtered_calls.append(call_data(**kept_data))
modified_record.samples = filtered_calls
return modified_record
def filter_all_sample_datatypes(records: list, *datatypes: str):
for record in records:
yield filter_sample_datatype(record, *datatypes)
def write_records_to_vcf(records: list, path: str):
with open(path, "w") as vcf_stream:
writer = vcf.Writer(vcf_stream, records[0])
for record in records:
writer.write_record(record)

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@ -1 +0,0 @@
# TODO Do stuff!

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from modvcfsamples.sample import filter_sample_datatype, filter_all_sample_datatypes, get_records_from_vcf
import os
def test_get_records_from_vcf_not_none():
records = get_records_from_vcf(os.path.abspath("tests/resources/test_files_shortened.vcf"))
assert len(records) > 0
def test_filter_sample_datatype_not_none():
records = get_records_from_vcf(os.path.abspath("tests/resources/test_files_shortened.vcf"))
filter_for = ["GT"]
modified_record = filter_sample_datatype(records[0], *filter_for)
assert modified_record is not None
def test_filter_sample_datatype_only_filtered():
records = get_records_from_vcf(os.path.abspath("tests/resources/test_files_shortened.vcf"))
filter_for = ["GT"]
modified_record = filter_sample_datatype(records[0], *filter_for)
for sample in modified_record.samples:
assert len(sample) <= len(filter_for)
for key, _ in sample._asdict().items():
assert key in filter_for
def test_filter_all_sample_datatypes_not_empty():
records = get_records_from_vcf(os.path.abspath("tests/resources/test_files_shortened.vcf"))
filter_for = ["GT"]
modified_records = list(filter_all_sample_datatypes(records, *filter_for))
assert len(modified_records) == 11
def test_filter_all_sample_datatypes_filtered():
records = get_records_from_vcf(os.path.abspath("tests/resources/test_files_shortened.vcf"))
filter_for = ["GT"]
modified_records = list(filter_all_sample_datatypes(records, *filter_for))
for modified_record in modified_records:
for sample in modified_record.samples:
assert len(sample) <= len(filter_for)
for key, _ in sample._asdict().items():
assert key in filter_for

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@ -1,2 +0,0 @@
# TODO Test program!

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##fileformat=VCFv4.1
##fileDate=10122015_22h01m13s
##source=SHAPEIT2.v837
##log_file=shapeit_10122015_22h01m13s_3f764d75-2fbb-42df-ab75-8c2dfd5731ce.log
##FORMAT=<ID=GT,Number=1,Type=String,Description="Phased Genotype">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Gambian Chinese French Brazilian Nigerian Pakistani English Colombian Indian Japanese
1 846808 rs4475691 C T 100 . AC=1276;AN=5008;DP=20368 GT:GQ:DP 1|1:70:60 0|0:30:10 0|0:20:40 ./.:0:0 0|0:70:60 0|0:90:30 0|0:80:70 0|0:50:80 ./.:0:0 0|0:100:80
1 846854 rs111957712 G A 100 . AC=114;AN=5008;DP=20538 GT:GQ:DP ./.:0:0 0|0:40:30 0|0:80:30 0|0:0:20 0|0:40:80 0|0:10:30 ./.:0:0 ./.:0:0 0|0:70:0 0|0:90:30
1 846864 rs950122 G C 100 . AC=1116;AN=5008;DP=20582 GT:GQ:DP 1|1:60:0 0|0:20:0 0|0:90:70 0|0:80:50 0|0:80:30 0|0:10:80 0|0:100:20 0|0:30:40 ./.:0:0 0|0:30:90
1 847228 rs3905286 C T 100 . AC=1215;AN=5008;DP=20731 GT:GQ:DP 1|1:70:80 0|0:90:80 0|0:60:50 0|0:60:90 0|0:30:40 0|0:70:10 0|0:100:80 0|0:100:50 0|1:70:100 0|0:40:40
1 847297 rs11507768 G A 100 . AC=359;AN=5008;DP=20809 GT:GQ:DP 1|0:0:60 0|0:10:30 0|0:80:60 ./.:0:0 0|0:10:100 0|0:10:100 ./.:0:0 0|0:100:40 0|0:20:20 0|0:10:0
1 847491 rs28407778 G A 100 . AC=1262;AN=5008;DP=16939 GT:GQ:DP 1|1:0:100 0|0:70:40 0|0:0:60 0|0:90:90 0|0:90:90 ./.:0:0 0|0:70:60 0|0:70:0 0|1:90:100 0|0:60:60
1 848023 rs144407116 C A 100 . AC=52;AN=5008;DP=22562 GT:GQ:DP 0|1:10:60 0|0:20:80 0|0:20:50 0|0:20:90 0|0:90:10 0|0:70:60 0|0:40:30 0|0:60:0 0|0:40:40 0|0:10:10
1 848090 rs4246505 G A 100 . AC=857;AN=5008;DP=19301 GT:GQ:DP 0|0:70:70 0|0:90:30 0|0:40:10 0|0:80:20 0|0:50:50 0|0:10:30 ./.:0:0 0|0:20:60 ./.:0:0 0|0:90:0
1 848445 rs4626817 G A 100 . AC=1255;AN=5008;DP=18444 GT:GQ:DP 1|1:100:40 0|0:80:90 0|0:30:100 0|0:100:60 0|0:40:90 0|0:20:30 0|0:70:100 ./.:0:0 ./.:0:0 0|0:80:30
1 848456 rs11507767 A G 100 . AC=1266;AN=5008;DP=18137 GT:GQ:DP 1|1:40:30 ./.:0:0 0|0:60:90 0|0:60:40 0|0:100:80 0|0:50:50 0|0:0:10 0|0:60:0 0|1:100:100 ./.:0:0
1 848738 rs3829741 C T 100 . AC=855;AN=5008;DP=16663 GT:GQ:DP 0|0:50:90 0|0:50:50 0|0:50:30 0|0:60:60 0|0:80:40 0|0:50:80 0|0:0:80 0|0:0:30 0|1:10:0 0|0:70:30