Added gt_nums, gt_bases, gt_type, phased to Call.

test/test_call.py

@@ -0,0 +1,18 @@
+import os
+import sys
+import vcf
+
+vcf_reader = vcf.VCFReader(open(sys.argv[1]), 'rb')
+for var in vcf_reader:
+    print var.CHROM, var.POS, var.REF, var.ALT
+    for sample in vcf_reader.samples:
+        if var.genotypes[sample].called:
+            print "\t", sample, \
+                  var.genotypes[sample].gt_nums, \
+                  var.genotypes[sample].gt_bases, \
+                  var.genotypes[sample].gt_type, \
+                  var.genotypes[sample].phased
+    print
+
+
+

vcf.py

@@ -230,13 +230,47 @@ def __init__(self, site, sample, data):
         self.site = site
         self.sample = sample
         self.data = data
+        self.gt_nums = self.data['GT']
+        self.called = self.gt_nums is not None
 
-    def called(self):
-        return self.GT != './.'
+    @property
+    def gt_bases(self):
+        '''Return the actual genotype alleles.
+           E.g. if VCF genotype is 0/1, return A/G
+        '''
+        # extract the numeric alleles of the gt string 
+        (a1, phase, a2) = list(self.gt_nums)
+        # lookup and return the actual DNA alleles
+        return self.site.alleles[int(a1)] + \
+               phase + \
+               self.site.alleles[int(a2)]
 
     @property
-    def GT(self):
-        return self.data['GT']
+    def gt_type(self):
+        '''Return the type of genotype.
+           hom_ref  = 0
+           het      = 1
+           hom_alt  = 2  (we don;t track _which+ ALT)
+           uncalled = None
+        '''
+        # extract the numeric alleles of the gt string
+        if self.called:
+            (a1, phase, a2) = list(self.gt_nums)
+            if (int(a1) == 0) and (int(a2) == 0): return 0
+            elif (int(a1) == 0) and (int(a2) >= 1): return 1
+            elif (int(a1) >= 1) and (int(a2) >= 1): return 2
+            else: return -1
+        else:
+            return None
+
+    @property
+    def phased(self):
+        '''Return a boolean indicating whether or not
+           the genotype is phased for this sample
+        '''
+        return self.data['GT'].find("|") >= 0
+
+
 
 
 class _Record(object):
@@ -251,7 +285,10 @@ def __init__(self, CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO, FORMAT, genotyp
         self.INFO = INFO
         self.FORMAT = FORMAT
         self.genotypes = genotypes
-
+        # create a list of alleles. [0] = REF, [1:] = ALTS
+        self.alleles = [self.REF]
+        self.alleles.extend(self.ALT)
+
     def __str__(self):
         return "Record(CHROM=%(CHROM)s, POS=%(POS)s, REF=%(REF)s, ALT=%(ALT)s)" % self.__dict__