phc-ingestion 0.8.26__py3-none-any.whl → 0.8.28__py3-none-any.whl

ingestion/nextgen/process.py

@@ -46,7 +46,7 @@ def process(
             prefix=case_id,
             log=log,
         )
-        structural_path_name = process_structural(
+        structural_path_name, translocations = process_structural(
             xml_in_file=vendor_files["xmlFile"],
             sv_in_file=vendor_files["somaticSvVcfFile"],
             root_path=local_output_dir,
@@ -59,6 +59,7 @@ def process(
             prefix=case_id,
             include_copy_number=bool(cnv_path_name),
             include_structural=bool(structural_path_name),
+            somatic_translocations=translocations,
             log=log,
         )
         pre_filtered_somatic_vcf_path = pre_filter_somatic_vcf(

ingestion/nextgen/util/nextgen_specific_genes.py

@@ -0,0 +1,29 @@
+from typing import TypedDict
+
+
+class GeneWithLocation(TypedDict):
+    gene: str
+    chr: str
+    start: int
+    end: int
+
+
+nextgen_specific_genes_with_location: list[GeneWithLocation] = [
+    {"gene": "IGK", "chr": "chr2", "start": 88852034, "end": 90258119},
+    {"gene": "NSD2", "chr": "chr4", "start": 1792518, "end": 1940193},
+    {"gene": "CCND3", "chr": "chr6", "start": 41920534, "end": 42562008},
+    {"gene": "MYC", "chr": "chr8", "start": 125309416, "end": 129673293},
+    {"gene": "CCND1", "chr": "chr11", "start": 69090733, "end": 69656860},
+    {"gene": "IGH", "chr": "chr14", "start": 105578834, "end": 109902208},
+    {"gene": "MAF", "chr": "chr16", "start": 78428398, "end": 79615096},
+    {"gene": "MAFB", "chr": "chr20", "start": 39039005, "end": 40688948},
+    {"gene": "IGL", "chr": "chr22", "start": 22012552, "end": 22965858},
+]
+nextgen_specific_genes: set[str] = {gene["gene"] for gene in nextgen_specific_genes_with_location}
+
+
+def maybe_get_matching_gene_for_location(chr: str, position: int) -> str | None:
+    for gene in nextgen_specific_genes_with_location:
+        if gene["chr"] == chr and gene["start"] <= position <= gene["end"]:
+            return gene["gene"]
+    return None

ingestion/nextgen/util/process_manifest.py

@@ -176,6 +176,7 @@ def process_manifest(
     prefix: str,
     include_copy_number: bool,
     include_structural: bool,
+    somatic_translocations: list[str],
     log: Logger,
 ):
     test_text = extract_xml_text(xml_in_file)
@@ -186,6 +187,8 @@ def process_manifest(
     hyperdiploidy_chromosomes = manifest_helpers.extract_hyperdiploidy_chromosomes(xml_in_file, log)
     if hyperdiploidy_chromosomes:
         manifest["hyperdiploidyTrisomies"] = hyperdiploidy_chromosomes
+    if somatic_translocations:
+        manifest["somaticTranslocations"] = somatic_translocations
 
     manifest["reportFile"] = f".lifeomic/nextgen/{prefix}/{prefix}.pdf"
     manifest["sourceFileId"] = source_file_id

ingestion/nextgen/util/process_structural.py

@@ -5,6 +5,10 @@ from typing import TypedDict
 from ingestion.shared_util.coords_to_genes import coords_to_genes
 from ingestion.nextgen.util.alteration_table import extract_variant_table
 from ingestion.nextgen.util.interpretation import map_interpretation
+from ingestion.nextgen.util.nextgen_specific_genes import (
+    maybe_get_matching_gene_for_location,
+    nextgen_specific_genes,
+)
 from ingestion.shared_util.open_maybe_gzipped import open_maybe_gzipped
 
 
@@ -42,9 +46,26 @@ def is_del_dup_or_ins(variant: list[str]) -> bool:
     return any([x in variant[2] for x in ["MantaDEL", "MantaDUP", "MantaINS"]])
 
 
+def get_gene_from_coords(
+    chromosome: str, start_position: str, end_position: str, log: Logger
+) -> str:
+    """
+    A number of genes of interest with specific start and end positions have been provided.
+    If a variant falls within the start and end positions of one of those genes of interest, that gene will be used.
+    Otherwise, we fall back to the standard gene lookup.
+    """
+    center_position = int((int(start_position) + int(end_position)) / 2)
+
+    gene = maybe_get_matching_gene_for_location(chromosome, center_position)
+    if gene:
+        return gene
+
+    return coords_to_genes("GRCh38", chromosome, center_position, log)
+
+
 def process_structural(
     sv_in_file: str, xml_in_file, root_path: str, prefix: str, log: Logger
-) -> str | None:
+) -> tuple[str | None, list[str]]:
     structural_variant_table = extract_variant_table(
         xml_in_file=xml_in_file, variant_type="structural", log=log
     )
@@ -74,9 +95,7 @@ def process_structural(
                 effect = "insertion"
 
             # Get genes from coordinates using center point of start and end positions
-            gene1 = coords_to_genes(
-                "GRCh38", chromosome1, int((int(start_position1) + int(end_position1)) / 2), log
-            )
+            gene1 = get_gene_from_coords(chromosome1, start_position1, end_position1, log)
             gene2 = "N/A"
 
         else:
@@ -89,12 +108,8 @@ def process_structural(
             effect = "translocation"
 
             # Get genes from coordinates using center point of start and end positions
-            gene1 = coords_to_genes(
-                "GRCh38", chromosome1, int((int(start_position1) + int(end_position1)) / 2), log
-            )
-            gene2 = coords_to_genes(
-                "GRCh38", chromosome2, int((int(start_position2) + int(end_position2)) / 2), log
-            )
+            gene1 = get_gene_from_coords(chromosome1, start_position1, end_position1, log)
+            gene2 = get_gene_from_coords(chromosome2, start_position2, end_position2, log)
 
         # Scrape interpretation
         interpretation = "unknown"
@@ -149,7 +164,7 @@ def process_structural(
 
     if not deduped_structural_variants:
         log.info(f"Ignoring empty structural variant file {sv_in_file}")
-        return None
+        return (None, [])
 
     log.info(f"Saving file to {structural_variant_path_name}")
     with open(structural_variant_path_name, "w+") as f:
@@ -159,4 +174,24 @@ def process_structural(
         for sv in deduped_structural_variants:
             f.write(structural_variant_to_csv_row(sv))
 
-    return structural_variant_path_name
+    log.info("Finding structural variant translocations for genes of interest")
+    translocations = [sv for sv in deduped_structural_variants if sv["effect"] == "translocation"]
+    formatted_translocations: set[str] = set()
+    for translocation in translocations:
+        gene1, gene2 = translocation["gene1"], translocation["gene2"]
+        # MYC is a special case
+        if gene1 == "MYC" or gene2 == "MYC":
+            formatted_translocations.add("t(MYC)")
+            continue
+        if gene1 in nextgen_specific_genes and gene2 in nextgen_specific_genes:
+            chr1, chr2 = int(translocation["position1"][0][3:]), int(
+                translocation["position2"][0][3:]
+            )
+            # Ensure chromosomes are in ascending order
+            if chr1 > chr2:
+                chr1, chr2 = chr2, chr1
+            formatted_translocations.add(f"t({chr1};{chr2})")
+
+    log.info(f"Found {len(formatted_translocations)} translocations for genes of interest")
+
+    return structural_variant_path_name, list(formatted_translocations)

{phc_ingestion-0.8.26.dist-info → phc_ingestion-0.8.28.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: phc-ingestion
-Version: 0.8.26
+Version: 0.8.28
 Summary: Functions for LifeOmic PHC genomic ingestions
 License: MIT
 Author-email: LifeOmic Development <development@lifeomic.com>

{phc_ingestion-0.8.26.dist-info → phc_ingestion-0.8.28.dist-info}/RECORD

@@ -29,14 +29,15 @@ ingestion/generic/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU
 ingestion/generic/process.py,sha256=WJHV_-SKhrDZ3JS3fm9DVMoW3Zs2t50GiraSV3vlLHE,1548
 ingestion/generic/utils.py,sha256=1MEIru7uq38IjUdL8lcHqDH0oTki9uWrz1f2e-pmRoU,2814
 ingestion/nextgen/__init__.py,sha256=7LQ-h_Bvc5P1QcHMdzsqi1Qm4fTJn04-ozar2ty9wSc,59
-ingestion/nextgen/process.py,sha256=GKiQ2dCxrR7tBD8TSP6Wk-TyoX3xBGip5zfpeT2buiQ,3782
+ingestion/nextgen/process.py,sha256=F0Ms8rTr_4boWPpE13D39C3ljFtyIVtw9XIIjCVI6f8,3849
 ingestion/nextgen/util/alteration_table.py,sha256=KwpJCQv_rVsL30jkzgZn0bKdd205fjVodYBNTcK3D1s,4220
 ingestion/nextgen/util/interpretation.py,sha256=ozuzb0vozff34zfP6AdOiUmI8Q77hI02jve_nCPZHfE,297
 ingestion/nextgen/util/manifest_helpers.py,sha256=PpSay-pe62jk735nom1tVD9nDE8-CxmzzCrgpBhgtjY,1571
+ingestion/nextgen/util/nextgen_specific_genes.py,sha256=II_E2AgAqv35u_ga25geRn6UHuZy_Uk9itfyu_HybFY,1211
 ingestion/nextgen/util/pre_filter_somatic_vcf.py,sha256=K_gH4EnUXrKB22u_f8FqQVGrOS5LxXNsNO3VBn381eY,2301
 ingestion/nextgen/util/process_cnv.py,sha256=m-AhsXFlYw4LTzgJJaj5vXYbK5n3H7cImzBxD2To6M0,2598
-ingestion/nextgen/util/process_manifest.py,sha256=TAbCHwN_2m08jySn1J4qEd9Nrxjw9CrsspwFWack0V4,8448
-ingestion/nextgen/util/process_structural.py,sha256=BXhwbRtFLTZsDi4ioSna1qmMtxVcsB0R-xNIvymm5Vw,5947
+ingestion/nextgen/util/process_manifest.py,sha256=FOa-m78layb5TFTktaDHkHT9hAGUeH9ZPGeqgBncz64,8585
+ingestion/nextgen/util/process_structural.py,sha256=sdAMcsgXm1lUbvNN6URSTwMfRoKDuOzPG2NFtKyhL0I,7593
 ingestion/nextgen/util/process_vcf.py,sha256=TvyV5wyXXSpFy2lc6h3ljqVQ5VeDPGxihHl2_K6LalQ,8432
 ingestion/nextgen/util/types.py,sha256=SSzt5gv-kss1PR45eQUelypWrGI-dAfQMO3GSD-T-Wg,22
 ingestion/resources/GRCh37_map.csv.gz,sha256=JOEkjtbYrJpIdyoZdCvfJhvvz2dNfkSve7lXSXkCCD8,408290
@@ -53,6 +54,6 @@ ingestion/vcf_standardization/util/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQe
 ingestion/vcf_standardization/util/af_helpers.py,sha256=dpTzoeIQVeBRt0ETF3a9rp5ojZqznHg4x_hCZ8OPcOg,1061
 ingestion/vcf_standardization/util/dp_helpers.py,sha256=Nq8oLOLObu4_pv16qwwgpALRlUoJVCULrd9cFOD-eoI,823
 ingestion/vcf_standardization/util/read_write.py,sha256=IQotJ27To1MoQcRstc5AbHZtUuJz5cqkkZiHsDNaBvI,2471
-phc_ingestion-0.8.26.dist-info/WHEEL,sha256=B19PGBCYhWaz2p_UjAoRVh767nYQfk14Sn4TpIZ-nfU,87
-phc_ingestion-0.8.26.dist-info/METADATA,sha256=e1BZcEIqQwMUSnYlBbGz4BLsHPYVZg8UOBOxbtxiZ-A,552
-phc_ingestion-0.8.26.dist-info/RECORD,,
+phc_ingestion-0.8.28.dist-info/WHEEL,sha256=B19PGBCYhWaz2p_UjAoRVh767nYQfk14Sn4TpIZ-nfU,87
+phc_ingestion-0.8.28.dist-info/METADATA,sha256=sNMcZ4aHN1IukmJRigUx9yGU-QMfnN9a7im0ULXoUcA,552
+phc_ingestion-0.8.28.dist-info/RECORD,,