ex-264 (cgates\dkriti) modifying how jacquard tags work

umich-brcf-bioinf · May 22, 2015 · ece8f5d · ece8f5d
1 parent 45be6dd
commit ece8f5d
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Showing 2 changed files with 39 additions and 3 deletions.
diff --git a/jacquard/variant_caller_transforms/common_tags.py b/jacquard/variant_caller_transforms/common_tags.py
@@ -1,6 +1,7 @@
 """Common tags used by several callers."""
 from __future__ import print_function, absolute_import, division
 import abc
+from abc import abstractmethod
 
 CALLER_REPORTED_TAG = "CALLER_REPORTED"
 CALLER_PASSED_TAG = "CALLER_PASSED"
@@ -9,6 +10,9 @@
 class JacquardTag(object):
     __metaclass__ = abc.ABCMeta
 
+    FORMAT = ('##FORMAT=<ID=JQ_{}_{},Number={},'
+                         'Type={},Description="{}">')
+
     class _TagType(object):
         def __init__(self, abbreviation, vcf_type, vcf_number):
             self.abbreviation = abbreviation
@@ -17,8 +21,18 @@ def __init__(self, abbreviation, vcf_type, vcf_number):
 
     DEPTH_TAG = _TagType("DP", "Integer", "1")
     GENOTYPE_TAG = _TagType("GT", "String", "A")
-
+    ALLELE_FREQ_TAG = _TagType("AF", "String", "A")
+    SOMATIC_TAG = _TagType("HC_SOM", "Integer", "1")
+
     def __init__(self, variant_caller_abbrev, tag_type, description):
+        self.metaheader = JacquardTag.FORMAT.format(variant_caller_abbrev,
+                                                    tag_type.abbreviation,
+                                                    tag_type.vcf_number,
+                                                    tag_type.vcf_type,
+                                                    description)
+
+    @abstractmethod
+    def add_tag_values(self):
         pass
 
 

diff --git a/test/variant_caller_transforms/common_tags_test.py b/test/variant_caller_transforms/common_tags_test.py
@@ -7,10 +7,10 @@
 
 
 class JacquardTagTestCase(test_case.JacquardBaseTestCase):
-    def xtest_allele_freq_tag(self):
+    def test_allele_freq_tag(self):
         tag = common_tags.JacquardTag.ALLELE_FREQ_TAG
         self.assertEquals("AF", tag.abbreviation)
-        self.assertEquals("Float", tag.vcf_type)
+        self.assertEquals("String", tag.vcf_type)
         self.assertEquals("A", tag.vcf_number)
 
     def test_depth_tag(self):
@@ -25,6 +25,28 @@ def test_genotype_tag(self):
         self.assertEquals("String", tag.vcf_type)
         self.assertEquals("A", tag.vcf_number)
 
+    def test_somatic_tag(self):
+        tag = common_tags.JacquardTag.SOMATIC_TAG
+        self.assertEquals("HC_SOM", tag.abbreviation)
+        self.assertEquals("Integer", tag.vcf_type)
+        self.assertEquals("1", tag.vcf_number)
+
+    def test_add_tag_values_is_abstract(self):
+        try:
+            class FakeTag(common_tags.JacquardTag):
+                def __init__(self): pass
+            FakeTag()
+            self.fail("Should not be able to instantiate JacquardTag without overrideing abstract methods.")
+        except TypeError: pass
+
+    def test_metaheader(self):
+        tag_type = common_tags.JacquardTag.GENOTYPE_TAG
+        class MyTag(common_tags.JacquardTag):
+            def add_tag_values(self, vcf_record): pass
+        actual_tag = MyTag("SK", tag_type, "foo bar baz")
+        expected_metaheader = '##FORMAT=<ID=JQ_SK_GT,Number=A,Type=String,Description="foo bar baz">'
+        self.assertEquals(expected_metaheader, actual_tag.metaheader)
+
 class ReportedTagTestCase(test_case.JacquardBaseTestCase):
     def test_reported_tag_metaheader(self):
         reported_tag = common_tags.ReportedTag("foo_")