phc-ingestion 0.10.16__py3-none-any.whl → 0.10.17__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/cnv.py +4 -2
- ingestion/foundation/util/fnv.py +4 -1
- {phc_ingestion-0.10.16.dist-info → phc_ingestion-0.10.17.dist-info}/METADATA +1 -1
- {phc_ingestion-0.10.16.dist-info → phc_ingestion-0.10.17.dist-info}/RECORD +5 -5
- {phc_ingestion-0.10.16.dist-info → phc_ingestion-0.10.17.dist-info}/WHEEL +0 -0
ingestion/foundation/util/cnv.py
CHANGED
|
@@ -42,13 +42,15 @@ def extract_copy_numbers(
|
|
|
42
42
|
log.info("Extracting copy numbers from xml")
|
|
43
43
|
copy_number_list: dict = {"CopyNumbers": []}
|
|
44
44
|
|
|
45
|
-
if
|
|
45
|
+
if (
|
|
46
|
+
"variant-report" in results_payload_dict
|
|
47
|
+
and "copy-number-alterations" in results_payload_dict["variant-report"].keys()
|
|
48
|
+
):
|
|
46
49
|
if (
|
|
47
50
|
results_payload_dict["variant-report"]["copy-number-alterations"] is not None
|
|
48
51
|
and "copy-number-alteration"
|
|
49
52
|
in results_payload_dict["variant-report"]["copy-number-alterations"].keys()
|
|
50
53
|
):
|
|
51
|
-
|
|
52
54
|
variants_dict = results_payload_dict["variant-report"]["copy-number-alterations"][
|
|
53
55
|
"copy-number-alteration"
|
|
54
56
|
]
|
ingestion/foundation/util/fnv.py
CHANGED
|
@@ -67,7 +67,10 @@ def extract_fusion_variant(
|
|
|
67
67
|
log.info("Extracting fusion variants from xml")
|
|
68
68
|
fusion_variant_list: dict = {"FusionVariants": []}
|
|
69
69
|
|
|
70
|
-
if
|
|
70
|
+
if (
|
|
71
|
+
"variant-report" in results_payload_dict
|
|
72
|
+
and "rearrangements" in results_payload_dict["variant-report"].keys()
|
|
73
|
+
):
|
|
71
74
|
if (
|
|
72
75
|
results_payload_dict["variant-report"]["rearrangements"] is not None
|
|
73
76
|
and "rearrangement" in results_payload_dict["variant-report"]["rearrangements"].keys()
|
|
@@ -18,8 +18,8 @@ ingestion/caris/util/vcf.py,sha256=Lkr4HnjMmMvEBVkD-9EkxRI3HpFmgCkgj6CXN4lBfIg,5
|
|
|
18
18
|
ingestion/foundation/__init__.py,sha256=CuUMsxSvWPAVzvnxx4hois632HpXwhwpjtMtiM98UoM,49
|
|
19
19
|
ingestion/foundation/process.py,sha256=mzKVVefGZD1HkEi0Hbb9eD_flwGp1S6SZ7FNXZpWnvI,2464
|
|
20
20
|
ingestion/foundation/util/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
|
|
21
|
-
ingestion/foundation/util/cnv.py,sha256=
|
|
22
|
-
ingestion/foundation/util/fnv.py,sha256
|
|
21
|
+
ingestion/foundation/util/cnv.py,sha256=eyTn1lqbo0tmEacnqWuGATt1h9lllTlVlboT8n5C6Ao,4283
|
|
22
|
+
ingestion/foundation/util/fnv.py,sha256=B8tOREYsR45aIGdSj8SPpe7f3L8FlGaIhLe0DSNqCnc,6006
|
|
23
23
|
ingestion/foundation/util/ga4gh.py,sha256=2oCTR9kvV5EeGZlrR35MfMkNL3nbeJYO88fo0NDDmRo,11304
|
|
24
24
|
ingestion/foundation/util/interpretation.py,sha256=LVVUmMyD6Un1rIKXqiyQDUC6oIJUd8cU3I9YHD5fsXg,405
|
|
25
25
|
ingestion/foundation/util/vcf_etl.py,sha256=GXV5JXswwdyHEEdPsM3Qq8tDPFkvZajrZn5chWgF53k,2266
|
|
@@ -59,6 +59,6 @@ ingestion/vcf_standardization/util/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQe
|
|
|
59
59
|
ingestion/vcf_standardization/util/af_helpers.py,sha256=dpTzoeIQVeBRt0ETF3a9rp5ojZqznHg4x_hCZ8OPcOg,1061
|
|
60
60
|
ingestion/vcf_standardization/util/dp_helpers.py,sha256=Nq8oLOLObu4_pv16qwwgpALRlUoJVCULrd9cFOD-eoI,823
|
|
61
61
|
ingestion/vcf_standardization/util/read_write.py,sha256=x3Pf6Dq8tmolblbCS5CrNmrcHS3FGfqBSFpFgvFGC4g,2526
|
|
62
|
-
phc_ingestion-0.10.
|
|
63
|
-
phc_ingestion-0.10.
|
|
64
|
-
phc_ingestion-0.10.
|
|
62
|
+
phc_ingestion-0.10.17.dist-info/WHEEL,sha256=B19PGBCYhWaz2p_UjAoRVh767nYQfk14Sn4TpIZ-nfU,87
|
|
63
|
+
phc_ingestion-0.10.17.dist-info/METADATA,sha256=qYPpPZAUmSeBfcZzMmYCAZrEmN7y01Hve1sKcGEtBSA,678
|
|
64
|
+
phc_ingestion-0.10.17.dist-info/RECORD,,
|
|
File without changes
|