Merge pull request jamescasbon#266 from sambrightman/called-definition

Allow partially-called genotypes to be considered called

Author: martijnvermaat

vcf/model.py

@@ -26,7 +26,7 @@ def __init__(self, site, sample, data):
         if getattr(self.data, 'GT', None) is not None:
             self.gt_alleles = [(al if al != '.' else None) for al in allele_delimiter.split(self.data.GT)]
             self.ploidity = len(self.gt_alleles)
-            self.called = all([al != None for al in self.gt_alleles])
+            self.called = any(al is not None for al in self.gt_alleles)
             self.gt_nums = self.data.GT if self.called else None
         else:
             #62 a call without a genotype is not defined as called or not
@@ -65,7 +65,7 @@ def gt_bases(self):
         if self.called:
             # lookup and return the actual DNA alleles
             try:
-                return self.gt_phase_char().join(str(self.site.alleles[int(X)]) for X in self.gt_alleles)
+                return self.gt_phase_char().join(str(self.site.alleles[int(X)] if X is not None else '.') for X in self.gt_alleles)
             except:
                 sys.stderr.write("Allele number not found in list of alleles\n")
         else:

vcf/test/test_vcf.py

@@ -1657,22 +1657,32 @@ def test_read_uncalled(self):
             gt_nums = [s.gt_nums for s in var.samples]
             ploidity = [s.ploidity for s in var.samples]
             gt_alleles = [s.gt_alleles for s in var.samples]
+            gt_type = [s.gt_type for s in var.samples]
 
             if var.POS == 14370:
                 self.assertEqual(['0|0', None, '1/1'], gt_nums)
                 self.assertEqual(['G|G', None, 'A/A'], gt_bases)
                 self.assertEqual([2,2,2], ploidity)
                 self.assertEqual([['0','0'], [None,None], ['1','1']], gt_alleles)
+                self.assertEqual([0, None, 2], gt_type)
             elif var.POS == 17330:
                 self.assertEqual([None, '0|1', '0/0'], gt_nums)
                 self.assertEqual([None, 'T|A', 'T/T'], gt_bases)
                 self.assertEqual([3,2,2], ploidity)
                 self.assertEqual([[None,None,None], ['0','1'], ['0','0']], gt_alleles)
+                self.assertEqual([None, 1, 0], gt_type)
             elif var.POS == 1234567:
                 self.assertEqual(['0/1', '0/2', None], gt_nums)
                 self.assertEqual(['GTC/G', 'GTC/GTCT', None], gt_bases)
                 self.assertEqual([2,2,1], ploidity)
                 self.assertEqual([['0','1'], ['0','2'], [None]], gt_alleles)
+                self.assertEqual([1, 1, None], gt_type)
+            elif var.POS == 1234568:
+                self.assertEqual(['./1', '0/.', None], gt_nums)
+                self.assertEqual(['./G', 'GTC/.', None], gt_bases)
+                self.assertEqual([2,2,1], ploidity)
+                self.assertEqual([[None,'1'], ['0',None], [None]], gt_alleles)
+                self.assertEqual([1, 1, None], gt_type)
         reader._reader.close()
 
 

vcf/test/uncalled_genotypes.vcf

@@ -5,3 +5,4 @@
 20	14370	rs6054257	G	A	29	PASS	NS=3	GT	0|0	./.	1/1
 20	17330	.	T	A	3	q10	NS=3	GT	././.	0|1	0/0
 20	1234567	microsat1	GTC	G,GTCT	50	PASS	NS=3	GT	0/1	0/2	.
+20	1234568	.	GTC	G,GTCT	50	PASS	NS=3	GT	./1	0/.	.