'Sequence.gc' Method for IUPAC bases

.github/workflows/main.yml

@@ -16,7 +16,7 @@ jobs:
       max-parallel: 10
       matrix:
         python-version: ['3.11', '3.10', '3.9', '3.8', '3.7']
-        os: [ubuntu, macos]
+        os: [ubuntu-latest, macos-latest]
         exclude:
           # mac os: exclude all but the last two (available) python releases
           - os: macos

.github/workflows/pypi.yml

@@ -7,7 +7,7 @@ on:
 jobs:
   build-n-publish:
     name: build and publish packages to PyPI and TestPyPI
-    runs-on: ubuntu
+    runs-on: ubuntu-latest
 
     steps:
       - name: checkout

pyfaidx/__init__.py

@@ -304,6 +304,34 @@ def gc(self):
         c = self.seq.count('C')
         c += self.seq.count('c')
         return (g + c) / len(self.seq)
+
+    @property
+    def gc_strict(self):
+        """ Return the GC content of seq as a float, ignoring non ACGT characters
+        >>> x = Sequence(name='chr1', seq='NMRATCGTA')
+        >>> y = round(x.gc, 2)
+        >>> y == 0.33
+        True
+        """
+        trimSeq = re.sub(r'[^ACGT]', '', self.seq.upper())
+        gc = sum(trimSeq.count(i) for i in ['G','C'])
+        return gc / len(trimSeq)
+
+    @property
+    def gc_iupac(self):
+        """ Return the GC content of seq as a float, accounting for IUPAC ambiguity 
+        >>> x = Sequence(name='chr1', seq='NMRATCGTA')
+        >>> y = round(x.gc, 2)
+        >>> y == 0.36
+        True
+        """
+        trimSeq = re.sub(r'[^ACGTMRWSYKVHDBN]', '', self.seq.upper())
+        gc =  sum(trimSeq.count(i) for i in ['S','C','G']) 
+        gc += sum(trimSeq.count(i) for i in ['B','V']) * 0.67
+        gc += sum(trimSeq.count(i) for i in ['M','R','Y','K']) * 0.5
+        gc += sum(trimSeq.count(i) for i in ['H','D']) * 0.33
+        gc += trimSeq.count('N') * 0.25
+        return gc / len(trimSeq)
 
 
 class IndexRecord(