translocation

src/pyphetools/__init__.py

@@ -4,7 +4,7 @@
 from . import visualization
 from . import validation
 
-__version__ = "0.9.84"
+__version__ = "0.9.85"
 
 __all__ = [
     "creation",

src/pyphetools/creation/import_template.py

@@ -121,6 +121,7 @@ def import_phenopackets_from_template(self,
                                         deletions:typing.Set[str]=set(),
                                         duplications:typing.Set[str]=set(),
                                         inversions:typing.Set[str]=set(),
+                                        translocations:typing.Set[str]=set(),
                                         hemizygous:bool=False,
                                         leniant_MOI:bool=False):
         """Import the data from an Excel template and create a collection of Phenopackets
@@ -134,6 +135,8 @@ def import_phenopackets_from_template(self,
         :type duplications: (typing.Set[str], optional
         :param inversions: Strings (identical to entries in the templates) that represent inversions.
         :type inversions: (typing.Set[str], optional
+        :param translocations: Strings (identical to entries in the templates) that represent translocations.
+        :type translocations: (typing.Set[str], optional
         :param hemizygous: Set this to true for X-chromosomal recessive conditions in which the genotype of affected males is hemizygous
         :type hemizygous: bool
         :param leniant_MOI: Do not check allelic requirements. Use this if the disease being curated has more than one MOI. This may require manually adding the "second" MOI in PhenoteFX
@@ -166,6 +169,8 @@ def import_phenopackets_from_template(self,
             vman.code_as_chromosomal_duplication(duplications)
         if len(inversions) > 0:
             vman.code_as_chromosomal_inversion(inversions)
+        if len(translocations) > 0:
+            vman.code_as_chromosomal_translocation(translocations)
         if vman.has_unmapped_alleles():
             mapped = vman.get_mapped_allele_count()
             print(f"We were able to map {mapped} alleles.")

src/pyphetools/creation/structural_variant.py

@@ -183,3 +183,30 @@ def chromosomal_inversion(cell_contents,
                                  sequence_ontology_id="SO:1000030",
                                  sequence_ontology_label="chromosomal_inversion",
                                  variant_id=variant_id)
+
+    @staticmethod
+    def chromosomal_translocation(cell_contents,
+                              gene_symbol,
+                              gene_id,
+                              genotype,
+                              variant_id=None):
+        """
+        create a StructuralVariant object for a chromosomal translocation
+
+        :param cell_contents: the string from the original table that we want to map as a structural variant
+        :type cell_contents: str
+        :param gene_symbol: the gene affected by the structural variant, e.g., GLI3
+        :type gene_symbol: str
+        :param gene_id: the identifier (using HGNC) of the gene, e.g., GLI3 is HGNC:4319
+        :type gene_id: str
+        :param genotype: Genotype (heterozygous, homozygous, hemizygous) of this variant call
+        :type genotype: str
+        :param variant_id: an identifier for the variant
+        :type variant_id: str, optional
+        """
+        return StructuralVariant(cell_contents=cell_contents,
+                                 gene_symbol=gene_symbol,
+                                 gene_id=gene_id,
+                                 sequence_ontology_id="SO:1000044",
+                                 sequence_ontology_label="chromosomal_translocation",
+                                 variant_id=variant_id)

src/pyphetools/creation/variant_manager.py

@@ -230,6 +230,21 @@ def code_as_chromosomal_inversion(self, allele_set) -> None:
             self._unmapped_alleles.remove(allele)
             self._var_d[allele] = var
 
+    def code_as_chromosomal_translocation(self, allele_set) -> None:
+        """
+        Code as Structural variants - chromosomal translocation (to be added to self._var_d)
+        :param allele_set: Set of alleles (strings) for coding as Structural variants (chromosomal inversion)
+        """
+        # first check that all of the alleles are in self._unmapped_alleles
+        if not allele_set.issubset(self._unmapped_alleles):
+            raise ValueError("[ERROR] We can only map alleles that were passed to the constructor - are you trying to map \"new\" alleles?")
+        if self._gene_id is None or self._gene_symbol is None:
+            raise ValueError("[ERROR] We cannot use this method unless the gene ID (HGNC) and symbol were passed to the constructor")
+        for allele in allele_set:
+            var = StructuralVariant.chromosomal_translocation(cell_contents=allele, gene_symbol=self._gene_symbol, gene_id=self._gene_id)
+            self._unmapped_alleles.remove(allele)
+            self._var_d[allele] = var
+
 
     def to_summary(self) -> pd.DataFrame:
         """