phc-ingestion 0.8.40__py3-none-any.whl → 0.8.42__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- ingestion/foundation/util/ga4gh.py +1 -1
- ingestion/generic/process.py +5 -1
- {phc_ingestion-0.8.40.dist-info → phc_ingestion-0.8.42.dist-info}/METADATA +1 -1
- {phc_ingestion-0.8.40.dist-info → phc_ingestion-0.8.42.dist-info}/RECORD +5 -5
- {phc_ingestion-0.8.40.dist-info → phc_ingestion-0.8.42.dist-info}/WHEEL +0 -0
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@@ -92,7 +92,7 @@ def get_plasma_tumor_fraction(genes) -> Optional[str]:
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ptf_val = ptf_entry.get("Alterations", {}).get("Alteration", {}).get("Name", "")
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try:
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# See https://github.com/lifeomic/phc-ingestion/pull/129
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-
float_val = float(ptf_val)
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float_val = float(ptf_val.strip("%"))
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if float_val > 0:
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return "Elevated"
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elif float_val == 0:
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ingestion/generic/process.py
CHANGED
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@@ -19,8 +19,12 @@ def process(
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vcf_final = base_vcf_file.replace(".vcf", ".modified.nrm.filtered.vcf")
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if not vcf_final.endswith(".gz"):
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vcf_final = vcf_final + ".gz"
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# All generic VCF ingestions are germline, so ensure the
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# sample name is prefixed with "germline_". This matches
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# the downstream logic in genomic-manifest
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sample_name = f"germline_{case_id}"
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vcf_line_count = standardize_vcf(
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vcf_file, vcf_out, out_path,
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vcf_file, vcf_out, out_path, sample_name, log, compression=True
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)
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# Add to manifest
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@@ -22,11 +22,11 @@ ingestion/foundation/process.py,sha256=T8YTvXRiThqE1LTERhrzvvD69mP4qJ7soJ1ZIbu8Y
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ingestion/foundation/util/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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ingestion/foundation/util/cnv.py,sha256=YSKCaOBhjZDNXth_GxC-50crDURpTNCMefoHo0uO7lQ,4215
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ingestion/foundation/util/fnv.py,sha256=-VstGsBKXM0duC-IpwUkektoTZ9yQUR0IQcDb1HibY0,5937
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-
ingestion/foundation/util/ga4gh.py,sha256=
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ingestion/foundation/util/ga4gh.py,sha256=dn7uoQdnKHfIVCSHVEyPpR0jc1uRp1YB4P_9tLMOxMs,11134
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ingestion/foundation/util/interpretation.py,sha256=LVVUmMyD6Un1rIKXqiyQDUC6oIJUd8cU3I9YHD5fsXg,405
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ingestion/foundation/util/vcf_etl.py,sha256=ZBrX1XGRz-ymLUEiVcjjqmPZPb-AfD9On8UkZJDa1Dk,2133
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ingestion/generic/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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-
ingestion/generic/process.py,sha256=
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ingestion/generic/process.py,sha256=ZaVnZ_gx9faDUsuresI1A0oCegTa-dPQT7DBFMeZGyY,1777
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ingestion/generic/utils.py,sha256=1MEIru7uq38IjUdL8lcHqDH0oTki9uWrz1f2e-pmRoU,2814
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ingestion/nextgen/__init__.py,sha256=7LQ-h_Bvc5P1QcHMdzsqi1Qm4fTJn04-ozar2ty9wSc,59
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ingestion/nextgen/process.py,sha256=5Z0RfclwTAYZruGDiLPutjPCYFh1DJpoWY9dnttghT4,3993
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@@ -54,6 +54,6 @@ ingestion/vcf_standardization/util/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQe
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ingestion/vcf_standardization/util/af_helpers.py,sha256=dpTzoeIQVeBRt0ETF3a9rp5ojZqznHg4x_hCZ8OPcOg,1061
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ingestion/vcf_standardization/util/dp_helpers.py,sha256=Nq8oLOLObu4_pv16qwwgpALRlUoJVCULrd9cFOD-eoI,823
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ingestion/vcf_standardization/util/read_write.py,sha256=x3Pf6Dq8tmolblbCS5CrNmrcHS3FGfqBSFpFgvFGC4g,2526
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phc_ingestion-0.8.
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phc_ingestion-0.8.
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phc_ingestion-0.8.
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phc_ingestion-0.8.42.dist-info/WHEEL,sha256=B19PGBCYhWaz2p_UjAoRVh767nYQfk14Sn4TpIZ-nfU,87
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phc_ingestion-0.8.42.dist-info/METADATA,sha256=LB_E096gDykQT0yFc3_AP28VNff1Zi91Ltj971FZ8c0,573
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phc_ingestion-0.8.42.dist-info/RECORD,,
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File without changes
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