phc-ingestion 0.8.30__py3-none-any.whl → 0.8.32__py3-none-any.whl

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Files changed (6) hide show
  1. ingestion/nextgen/util/alteration_table.py +2 -0
  2. ingestion/nextgen/util/process_structural.py +2 -0
  3. ingestion/nextgen/util/process_vcf.py +1 -1
  4. {phc_ingestion-0.8.30.dist-info → phc_ingestion-0.8.32.dist-info}/METADATA +1 -1
  5. {phc_ingestion-0.8.30.dist-info → phc_ingestion-0.8.32.dist-info}/RECORD +6 -6
  6. {phc_ingestion-0.8.30.dist-info → phc_ingestion-0.8.32.dist-info}/WHEEL +0 -0
ingestion/nextgen/util/alteration_table.py CHANGED
@@ -15,6 +15,8 @@ short_variant_types: list[str] = [
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  "Splice site",
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  "Splice region",
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  "Nonsense",
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+ "Splice acceptor",
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+ "Splice donor",
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  ]
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ingestion/nextgen/util/process_structural.py CHANGED
@@ -181,6 +181,8 @@ def process_structural(
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  gene1, gene2 = translocation["gene1"], translocation["gene2"]
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  # MYC is a special case
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  if gene1 == "MYC" or gene2 == "MYC":
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+ if gene1 == gene2:
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+ continue
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  formatted_translocations.add("t(MYC)")
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  continue
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  if gene1 in nextgen_specific_genes and gene2 in nextgen_specific_genes:
ingestion/nextgen/util/process_vcf.py CHANGED
@@ -206,7 +206,7 @@ def process_vcf(
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  def map_vendsig(vendsig: str) -> str:
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  if vendsig in ["Pathogenic"]:
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  return "VENDSIG=Pathogenic"
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- elif vendsig in ["Likely Pathogenic"]:
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+ elif vendsig in ["Likely Pathogenic", "LikelyPathogenic"]:
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  return "VENDSIG=Likely pathogenic"
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  elif vendsig in ["VUS"]:
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  return "VENDSIG=Uncertain significance"
{phc_ingestion-0.8.30.dist-info → phc_ingestion-0.8.32.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: phc-ingestion
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- Version: 0.8.30
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+ Version: 0.8.32
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  Summary: Functions for LifeOmic PHC genomic ingestions
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  License: MIT
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  Author-email: LifeOmic Development <development@lifeomic.com>
{phc_ingestion-0.8.30.dist-info → phc_ingestion-0.8.32.dist-info}/RECORD RENAMED
@@ -30,15 +30,15 @@ ingestion/generic/process.py,sha256=WJHV_-SKhrDZ3JS3fm9DVMoW3Zs2t50GiraSV3vlLHE,
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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=F0Ms8rTr_4boWPpE13D39C3ljFtyIVtw9XIIjCVI6f8,3849
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- ingestion/nextgen/util/alteration_table.py,sha256=KwpJCQv_rVsL30jkzgZn0bKdd205fjVodYBNTcK3D1s,4220
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+ ingestion/nextgen/util/alteration_table.py,sha256=h3nqImVRGgMV62P5_8wZBbaD06lr7kJA9JOBqtW3fco,4263
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  ingestion/nextgen/util/interpretation.py,sha256=ozuzb0vozff34zfP6AdOiUmI8Q77hI02jve_nCPZHfE,297
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  ingestion/nextgen/util/manifest_helpers.py,sha256=PpSay-pe62jk735nom1tVD9nDE8-CxmzzCrgpBhgtjY,1571
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  ingestion/nextgen/util/nextgen_specific_genes.py,sha256=II_E2AgAqv35u_ga25geRn6UHuZy_Uk9itfyu_HybFY,1211
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  ingestion/nextgen/util/pre_filter_somatic_vcf.py,sha256=K_gH4EnUXrKB22u_f8FqQVGrOS5LxXNsNO3VBn381eY,2301
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  ingestion/nextgen/util/process_cnv.py,sha256=m-AhsXFlYw4LTzgJJaj5vXYbK5n3H7cImzBxD2To6M0,2598
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  ingestion/nextgen/util/process_manifest.py,sha256=FOa-m78layb5TFTktaDHkHT9hAGUeH9ZPGeqgBncz64,8585
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- ingestion/nextgen/util/process_structural.py,sha256=56wVGmZIfQwqNYthCZ4OdFAaqkoZKZvIpJtf-wekzg4,7647
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- ingestion/nextgen/util/process_vcf.py,sha256=TvyV5wyXXSpFy2lc6h3ljqVQ5VeDPGxihHl2_K6LalQ,8432
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+ ingestion/nextgen/util/process_structural.py,sha256=fUhoVGY5XHXPqLjC9bKD8JpXNDF9VbUQGl3Y3d7vG6E,7703
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+ ingestion/nextgen/util/process_vcf.py,sha256=H2Jd5CzQiTBOjk3w95LuPp2rN79bKHBrMRDjG-YNTXE,8452
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  ingestion/nextgen/util/types.py,sha256=SSzt5gv-kss1PR45eQUelypWrGI-dAfQMO3GSD-T-Wg,22
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  ingestion/resources/GRCh37_map.csv.gz,sha256=JOEkjtbYrJpIdyoZdCvfJhvvz2dNfkSve7lXSXkCCD8,408290
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  ingestion/resources/GRCh38_map.csv.gz,sha256=qriYO2_buCCb4T6WcuZ-pCwPxMsm0TL2OxAHvJ1cEfA,612373
@@ -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=IQotJ27To1MoQcRstc5AbHZtUuJz5cqkkZiHsDNaBvI,2471
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- phc_ingestion-0.8.30.dist-info/WHEEL,sha256=B19PGBCYhWaz2p_UjAoRVh767nYQfk14Sn4TpIZ-nfU,87
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- phc_ingestion-0.8.30.dist-info/METADATA,sha256=INHa_HPURw_yLwcvBNcToW67OJsFgEJBNWwfr1GtGzw,552
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- phc_ingestion-0.8.30.dist-info/RECORD,,
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+ phc_ingestion-0.8.32.dist-info/WHEEL,sha256=B19PGBCYhWaz2p_UjAoRVh767nYQfk14Sn4TpIZ-nfU,87
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+ phc_ingestion-0.8.32.dist-info/METADATA,sha256=dOeze5ldcBfhTefz5dF0weoa71CgORwhYWFGl8JAEPg,552
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+ phc_ingestion-0.8.32.dist-info/RECORD,,