gumpy - pypi Package Compare versions

Comparing version 1.3.1 to 1.3.2

gumpy.egg-info/PKG-INFO

 Metadata-Version: 2.1
 Name: gumpy
-Version: 1.3.1
+Version: 1.3.2
 Summary: Genetics with Numpy
@@ -10,3 +10,2 @@ Home-page: https://github.com/oxfordmmm/gumpy
 Classifier: Programming Language :: Python :: 3
-Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
@@ -13,0 +12,0 @@ Requires-Python: >=3.10

gumpy/difference.py

@@ -194,3 +194,3 @@ """
         self, gene: str, idx: int, variant: str, start: int | None = None
-    ) -> int:
+    ) -> int | None:
         """Find the gene position of a given nucleotide index.
@@ -207,3 +207,4 @@ This is considerably faster than building a whole stacked_gene_pos array
         Returns:
-            int: Gene position of this nucleotide index
+            int | None: Gene position of this nucleotide index
+                        (or None if it lies outside of the gene)
         """
@@ -244,2 +245,12 @@ stacked_gene_mask = self.genome1.stacked_gene_name == gene
 
+                # Edge case of deletion starting in revcomp gene and extending
+                # past gene start, so return None
+                if (
+                    self.genome2.stacked_nucleotide_number[
+                        self.genome2.stacked_gene_name == gene
+                    ][-1]
+                    > nc_num
+                ):
+                    return None
+
         return nc_num
@@ -409,3 +420,7 @@
                     gene_pos.append(self.get_gene_pos(gene, idx, variants[-1]))
-                    if self.genome2.genes[gene]["codes_protein"] and gene_pos[-1] > 0:
+                    if (
+                        self.genome2.genes[gene]["codes_protein"]
+                        and gene_pos[-1] is not None
+                        and gene_pos[-1] > 0
+                    ):
                         # Get codon idx
@@ -445,3 +460,7 @@ nc_idx = self.genome1.stacked_nucleotide_index[
 
-                    if self.genome2.genes[gene]["codes_protein"] and gene_pos[-1] > 0:
+                    if (
+                        self.genome2.genes[gene]["codes_protein"]
+                        and gene_pos[-1] is not None
+                        and gene_pos[-1] > 0
+                    ):
                         # Get codon idx
@@ -561,2 +580,3 @@ nc_idx = self.genome1.stacked_nucleotide_index[
                             self.genome2.genes[gene]["codes_protein"]
+                            and gene_pos[-1] is not None
                             and gene_pos[-1] > 0
@@ -608,2 +628,3 @@ ):
                             self.genome2.genes[gene]["codes_protein"]
+                            and gene_pos[-1] is not None
                             and gene_pos[-1] > 0
@@ -720,2 +741,3 @@ ):
                             self.genome2.genes[gene]["codes_protein"]
+                            and gene_pos[-1] is not None
                             and gene_pos[-1] > 0
@@ -767,2 +789,3 @@ ):
                             self.genome2.genes[gene]["codes_protein"]
+                            and gene_pos[-1] is not None
                             and gene_pos[-1] > 0
@@ -769,0 +792,0 @@ ):

PKG-INFO

 Metadata-Version: 2.1
 Name: gumpy
-Version: 1.3.1
+Version: 1.3.2
 Summary: Genetics with Numpy
@@ -10,3 +10,2 @@ Home-page: https://github.com/oxfordmmm/gumpy
 Classifier: Programming Language :: Python :: 3
-Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
@@ -13,0 +12,0 @@ Requires-Python: >=3.10

setup.cfg

@@ -12,3 +12,2 @@ [metadata]
 	Programming Language :: Python :: 3
-	License :: OSI Approved :: MIT License
 	Operating System :: OS Independent
@@ -15,0 +14,0 @@ license = University of Oxford, see LICENSE.md

VERSION

@@ -1,2 +0,2 @@
-1.3.1
+1.3.2
 

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Improved metrics

Total package byte prevSize

208249

0.38%

Lines of code

4075

0.54%