phc-ingestion 0.8.29__py3-none-any.whl → 0.8.31__py3-none-any.whl

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Files changed (6) hide show
  1. ingestion/caris/util/structural.py +1 -1
  2. ingestion/nextgen/util/alteration_table.py +2 -0
  3. ingestion/nextgen/util/process_structural.py +2 -0
  4. {phc_ingestion-0.8.29.dist-info → phc_ingestion-0.8.31.dist-info}/METADATA +1 -1
  5. {phc_ingestion-0.8.29.dist-info → phc_ingestion-0.8.31.dist-info}/RECORD +6 -6
  6. {phc_ingestion-0.8.29.dist-info → phc_ingestion-0.8.31.dist-info}/WHEEL +0 -0
ingestion/caris/util/structural.py CHANGED
@@ -33,7 +33,7 @@ def extract_structural(prefix, data, log: Logger):
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  "no result",
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  "indeterminate",
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  "wild type",
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- "hlaVD",
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+ "hlavd",
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  ]:
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  structural_variant_tests.append(this_result)
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  if not structural_variant_tests:
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:
{phc_ingestion-0.8.29.dist-info → phc_ingestion-0.8.31.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: 0.8.29
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+ Version: 0.8.31
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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-0.8.29.dist-info → phc_ingestion-0.8.31.dist-info}/RECORD RENAMED
@@ -11,7 +11,7 @@ ingestion/caris/util/interpretation.py,sha256=CghNurqeVA5VTBBorU8-ZTN-PVNPnR8wrm
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  ingestion/caris/util/json.py,sha256=xVEfwKOwyRCEXZWKr9zXooPIrxGkUtSxcAYuDUHkAxw,4706
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  ingestion/caris/util/metadata.py,sha256=629-yPh_qIZKJCJzJHEvo6EUGxIBW3Gw31RSytF4v08,9541
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  ingestion/caris/util/specimen_details.py,sha256=R3uKHlLR056XcQbUPI6IO2dLr-z5Z5AJi866DJ379Qw,2105
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- ingestion/caris/util/structural.py,sha256=yE-okF59OoIULBB7JQHHcrRHghiPoNyG2LCtknm0C2E,4628
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+ ingestion/caris/util/structural.py,sha256=EUcMIea_WnafoVmFLIyEqlJ_HtYIj_g6qkekXa7QNQs,4628
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  ingestion/caris/util/tar.py,sha256=BGR_2vBbxyMgF-GzJ3SrihsPdOzII4SFVz9tvKV5vo0,482
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  ingestion/caris/util/tests.py,sha256=mcG3A8TW81_sn2Bfoa-Gd6Q1sR3_R4FX2BNskD4DkJk,372
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  ingestion/caris/util/tmb.py,sha256=DVi1wPSjVr_32ZCc6Yb51tGqUlcxUx40yCvuqvNuDx4,1027
@@ -30,14 +30,14 @@ 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_structural.py,sha256=fUhoVGY5XHXPqLjC9bKD8JpXNDF9VbUQGl3Y3d7vG6E,7703
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  ingestion/nextgen/util/process_vcf.py,sha256=TvyV5wyXXSpFy2lc6h3ljqVQ5VeDPGxihHl2_K6LalQ,8432
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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
@@ -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-0.8.29.dist-info/WHEEL,sha256=B19PGBCYhWaz2p_UjAoRVh767nYQfk14Sn4TpIZ-nfU,87
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- phc_ingestion-0.8.29.dist-info/METADATA,sha256=yaQSargO2FJ9_mR6PJ5mRTTYXPhUIailySSuH-wBsxg,552
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- phc_ingestion-0.8.29.dist-info/RECORD,,
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+ phc_ingestion-0.8.31.dist-info/WHEEL,sha256=B19PGBCYhWaz2p_UjAoRVh767nYQfk14Sn4TpIZ-nfU,87
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+ phc_ingestion-0.8.31.dist-info/METADATA,sha256=2b0ZTRMP3dMucsx_0wMtLBripA-ak7EgMZsGCUbhT24,552
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+ phc_ingestion-0.8.31.dist-info/RECORD,,