phc-ingestion 0.8.38__py3-none-any.whl → 0.8.39__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.
Files changed (6) hide show
  1. ingestion/nextgen/util/alteration_table.py +2 -2
  2. ingestion/nextgen/util/interpretation.py +6 -1
  3. ingestion/nextgen/util/manifest_helpers.py +1 -1
  4. {phc_ingestion-0.8.38.dist-info → phc_ingestion-0.8.39.dist-info}/METADATA +1 -1
  5. {phc_ingestion-0.8.38.dist-info → phc_ingestion-0.8.39.dist-info}/RECORD +6 -6
  6. {phc_ingestion-0.8.38.dist-info → phc_ingestion-0.8.39.dist-info}/WHEEL +0 -0
ingestion/nextgen/util/alteration_table.py CHANGED
@@ -122,7 +122,7 @@ def extract_alteration_table_rows(xml_in_file: str, log: Logger) -> list[Alterat
122
122
 
123
123
 
124
124
  def parse_short_variant_gene(gene: str) -> ShortVariantGene:
125
- pattern = r"^.*\((?P<chr>chr\d+|chrX|chrY):(?P<pos>\d+).*\).*$"
125
+ pattern = r"^.*\((?P<chr>chr\d+|chrX|chrY):(?P<pos>\d+).*$"
126
126
  match = re.match(pattern, gene)
127
127
  if not match:
128
128
  raise RuntimeError(f"Failed to parse gene field for short variant")
@@ -143,7 +143,7 @@ def parse_copy_number_variant_gene(gene: str) -> CopyNumberVariantGene:
143
143
 
144
144
 
145
145
  def parse_structural_variant_gene(gene: str) -> StructuralVariantGene:
146
- pattern = r"^(?P<gene1>[A-Z1-9]*)(-|\/)(?P<gene2>[A-Z1-9]*).*\(.*(?P<chr1>chr\d+|chrX|chrY):(?P<pos1>\d+).*;.*(?P<chr2>chr\d+|chrX|chrY):(?P<pos2>\d+).*\).*$"
146
+ pattern = r"^\*?(?P<gene1>[A-Z1-9]*)(-|\/|:+)(?P<gene2>[A-Z1-9]*).*\(.*(?P<chr1>chr\d+|chrX|chrY):(?P<pos1>\d+).*;.*(?P<chr2>chr\d+|chrX|chrY):(?P<pos2>\d+).*\).*$"
147
147
  match = re.match(pattern, gene)
148
148
  if not match:
149
149
  raise RuntimeError(f"Failed to parse gene field for structural variant")
ingestion/nextgen/util/interpretation.py CHANGED
@@ -21,7 +21,12 @@ def map_vendsig(vendsig: str) -> str:
21
21
  vendsig_lower = vendsig.lower()
22
22
  if vendsig_lower in ["pathogenic"]:
23
23
  return "VENDSIG=Pathogenic"
24
- elif vendsig_lower in ["likely pathogenic", "likelypathogenic"]:
24
+ elif vendsig_lower in [
25
+ "likely pathogenic",
26
+ "likelypathogenic",
27
+ "likey pathogenic",
28
+ "likeypathogenic",
29
+ ]:
25
30
  return "VENDSIG=Likely pathogenic"
26
31
  elif vendsig_lower in ["vus"]:
27
32
  return "VENDSIG=Uncertain significance"
ingestion/nextgen/util/manifest_helpers.py CHANGED
@@ -25,7 +25,7 @@ def parse_patient_name(line: str) -> str:
25
25
 
26
26
 
27
27
  def parse_sample_number(line: str) -> str:
28
- return parse_pattern(r"^.*Specimen #: (\d*) .*$", line, "sample number")
28
+ return parse_pattern(r"^.*Specimen #: (\d*-?R?) .*$", line, "sample number")
29
29
 
30
30
 
31
31
  def parse_body_site(line: str) -> str:
{phc_ingestion-0.8.38.dist-info → phc_ingestion-0.8.39.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.1
2
2
  Name: phc-ingestion
3
- Version: 0.8.38
3
+ Version: 0.8.39
4
4
  Summary: Functions for LifeOmic PHC genomic ingestions
5
5
  License: MIT
6
6
  Author-email: LifeOmic Development <development@lifeomic.com>
{phc_ingestion-0.8.38.dist-info → phc_ingestion-0.8.39.dist-info}/RECORD RENAMED
@@ -30,9 +30,9 @@ ingestion/generic/process.py,sha256=WJHV_-SKhrDZ3JS3fm9DVMoW3Zs2t50GiraSV3vlLHE,
30
30
  ingestion/generic/utils.py,sha256=1MEIru7uq38IjUdL8lcHqDH0oTki9uWrz1f2e-pmRoU,2814
31
31
  ingestion/nextgen/__init__.py,sha256=7LQ-h_Bvc5P1QcHMdzsqi1Qm4fTJn04-ozar2ty9wSc,59
32
32
  ingestion/nextgen/process.py,sha256=5Z0RfclwTAYZruGDiLPutjPCYFh1DJpoWY9dnttghT4,3993
33
- ingestion/nextgen/util/alteration_table.py,sha256=bvTrXEhIRye5BzSXjZEBy1AvXLZgG0rNkNt3e3rcvv0,6127
34
- ingestion/nextgen/util/interpretation.py,sha256=56wVk9j-w59gM-11iODXbKuUtZcEwe8zJQSXpjyCguw,872
35
- ingestion/nextgen/util/manifest_helpers.py,sha256=LH5em0xsu9Hrs175vfx6SX8W1Ww2FFRp2wIBSfIEMUM,2725
33
+ ingestion/nextgen/util/alteration_table.py,sha256=JTWBL1Fqj_pGsH5vwuVEnCUJle2wOBk6VYImHYCF9vg,6129
34
+ ingestion/nextgen/util/interpretation.py,sha256=a_B8jVjJXjkrN0hNzB260WNlZdY-BkL26LyLZcYP20A,950
35
+ ingestion/nextgen/util/manifest_helpers.py,sha256=zucNhbSss6IuU-kf3tpVoSxV27iSNQohGSMUXQQePSc,2729
36
36
  ingestion/nextgen/util/nextgen_specific_genes.py,sha256=1jFcqvtYAlJ7eBwOBm1UC2TzAbjHjdlvPBUzxr1G8dY,1206
37
37
  ingestion/nextgen/util/pre_filter_somatic_vcf.py,sha256=mIaUihmGLbS38D4Gy_Qtf1lFAfW0A-LgAgQmsrEiI-M,3529
38
38
  ingestion/nextgen/util/process_cnv.py,sha256=MIirc8e0k6lsaTZkRM3U3L3IvbrcHmKQ4xlIu585514,2430
@@ -54,6 +54,6 @@ ingestion/vcf_standardization/util/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQe
54
54
  ingestion/vcf_standardization/util/af_helpers.py,sha256=dpTzoeIQVeBRt0ETF3a9rp5ojZqznHg4x_hCZ8OPcOg,1061
55
55
  ingestion/vcf_standardization/util/dp_helpers.py,sha256=Nq8oLOLObu4_pv16qwwgpALRlUoJVCULrd9cFOD-eoI,823
56
56
  ingestion/vcf_standardization/util/read_write.py,sha256=x3Pf6Dq8tmolblbCS5CrNmrcHS3FGfqBSFpFgvFGC4g,2526
57
- phc_ingestion-0.8.38.dist-info/WHEEL,sha256=B19PGBCYhWaz2p_UjAoRVh767nYQfk14Sn4TpIZ-nfU,87
58
- phc_ingestion-0.8.38.dist-info/METADATA,sha256=zGjelnmcC8NGRJa7qsZmKB6ifrwH1v6PjlR3RDwZ9vs,573
59
- phc_ingestion-0.8.38.dist-info/RECORD,,
57
+ phc_ingestion-0.8.39.dist-info/WHEEL,sha256=B19PGBCYhWaz2p_UjAoRVh767nYQfk14Sn4TpIZ-nfU,87
58
+ phc_ingestion-0.8.39.dist-info/METADATA,sha256=ogeBhWcNlAxc4jcbteveRr-zJYhlQASc9UgZbJnF0Wc,573
59
+ phc_ingestion-0.8.39.dist-info/RECORD,,