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Updated pipeline and formatted code
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Pipeline now looks for correct unit test file
This commit is contained in:
Harrison Deng
2023-06-27 14:15:03 +00:00
parent 58adf3efe8
commit 8cd09bfb41
3 changed files with 24 additions and 8 deletions
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28
tests/modvcfsamples/test_sample.py
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@@ -1,14 +1,24 @@
from modvcfsamples.sample import keep_specific_call_data, get_records_from_vcf, normalize_gt_to_length
from modvcfsamples.sample import (
keep_specific_call_data,
get_records_from_vcf,
normalize_gt_to_length,
)
import os
def test_filter_all_sample_datatypes_not_empty():
records, header = get_records_from_vcf(os.path.abspath("tests/resources/test_files_shortened.vcf"))
records, header = get_records_from_vcf(
os.path.abspath("tests/resources/test_files_shortened.vcf")
)
filter_for = ["GT"]
modified_records, header = keep_specific_call_data(records, header, *filter_for)
assert len(modified_records) == 11
def test_filter_all_sample_datatypes_filtered():
records, header = get_records_from_vcf(os.path.abspath("tests/resources/test_files_shortened.vcf"))
records, header = get_records_from_vcf(
os.path.abspath("tests/resources/test_files_shortened.vcf")
)
filter_for = ["GT"]
modified_records, header = keep_specific_call_data(records, header, *filter_for)
for modified_record in modified_records:
@@ -17,14 +27,20 @@ def test_filter_all_sample_datatypes_filtered():
for key, _ in call.data.items():
assert key in filter_for
def test_normalize_gt_to_length_not_empty():
records, header = get_records_from_vcf(os.path.abspath("tests/resources/test_files_shortened_haploid.vcf"))
records, header = get_records_from_vcf(
os.path.abspath("tests/resources/test_files_shortened_haploid.vcf")
)
modified_records, _ = normalize_gt_to_length(records, header, 4)
assert len(modified_records) > 0
def test_normalize_gt_to_length_gt_normalized():
records, header = get_records_from_vcf(os.path.abspath("tests/resources/test_files_shortened_haploid.vcf"))
records, header = get_records_from_vcf(
os.path.abspath("tests/resources/test_files_shortened_haploid.vcf")
)
modified_records, _ = normalize_gt_to_length(records, header, 4)
for modified_record in modified_records:
for call in modified_record.calls:
assert len(call.data["GT"].split("|")) == 4 or "/" in call.data["GT"]
assert len(call.data["GT"].split("|")) == 4 or "/" in call.data["GT"]