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Switch from PyVCF to PyVCF3 and update workflow to install dependencies from requirements.txt #103

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May 26, 2022
Merged

Switch from PyVCF to PyVCF3 and update workflow to install dependencies from requirements.txt #103

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aff47ed
Switch from PyVCF to PyVCF3
Rohan-cod May 26, 2022
2b82949
Update workflow to install dependencies from requirements.txt
Rohan-cod May 26, 2022
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4 changes: 2 additions & 2 deletions .github/workflows/main.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ jobs:
run: python -m pip install --upgrade pip
- name: Install cython wheel
run: pip install cython wheel
- name: Install vcf2fhir
run: pip install vcf2fhir
- name: Install Dependencies
run: pip install -r requirements.txt
- name: Run Unit tests
run: python -m unittest
7 changes: 7 additions & 0 deletions requirements.txt
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@@ -0,0 +1,7 @@
Cython>=0.29.21
fhirclient==3.2.0
pysam
pandas
pytz>=2019.3
PyVCF3>=1.0.3
pyranges>=0.0.96
2 changes: 1 addition & 1 deletion setup.cfg
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Expand Up @@ -28,7 +28,7 @@ install_requires =
pysam
pandas
pytz>=2019.3
pyVCF>=0.6.8
PyVCF3>=1.0.3
pyranges>=0.0.96
tests_require =
unittest
10 changes: 8 additions & 2 deletions vcf2fhir/fhir_helper.py
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Expand Up @@ -82,7 +82,10 @@ def _add_phase_records(self, record):
if(sample_data.GT is not None and
len(sample_data.GT.split('|')) >= 2 and
'PS' in sample_data._fields):
self.phased_rec_map.setdefault(sample_data.PS, []).append(record)
sample_data_ps = sample_data.PS
if isinstance(sample_data.PS, list):
sample_data_ps = sample_data_ps[0]
self.phased_rec_map.setdefault(sample_data_ps, []).append(record)

def initalize_report(self):
patient_reference = reference.FHIRReference(
Expand Down Expand Up @@ -266,12 +269,15 @@ def add_variant_obv(
"http://loinc.org", "82155-3",
"Genomic Structural Variant copy Number"
)
copy_number = record.samples[0]["CN"]
if isinstance(record.samples[0]["CN"], list):
copy_number = copy_number[0]
copy_number_component\
.valueQuantity = quantity.Quantity(
{
"system": "http://unitsofmeasure.org",
"code": '1',
"value": record.samples[0]["CN"]
"value": copy_number
}
)

Expand Down