ex-266 (jebene/dkriti/cgates) began work on TagRegistry

umich-brcf-bioinf · May 28, 2015 · ec745fe · ec745fe
1 parent 057dd86
commit ec745fe
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diff --git a/jacquard/merge.py b/jacquard/merge.py
@@ -97,6 +97,28 @@ def _get_next(self):
         except StopIteration:
             return None
 
+class TagRegistry(object):
+    def __init__(self):
+        self.metaheaders = {}
+
+
+    @staticmethod
+    def _passthrough(tag_id, metaheader):
+        return tag_id.startswith('JQ_') or \
+                   not metaheader.startswith('##FORMAT=<')
+
+    def register_tag(self, tag_id, metaheader):
+        if self._passthrough(tag_id, metaheader):
+            new_tag_id = tag_id
+        else:
+            if metaheader not in self.metaheaders:
+                new_tag = 'JX{}_{}'.format(len(self.metaheaders) + 1, tag_id)
+                self.metaheaders[metaheader] = new_tag
+
+            new_tag_id = self.metaheaders[metaheader]
+        return new_tag_id
+
+
 class NewMergeVcfReader(vcf.VcfReader):
     def __init__(self, file_reader, format_tag_mapping):
         super(self.__class__,self).__init__(file_reader)

diff --git a/jacquard/utils/vcf.py b/jacquard/utils/vcf.py
@@ -34,6 +34,15 @@ def _get_tag_metaheaders(self, regex_exp):
 
         return tag_dict
 
+    @classmethod
+    def get_id_from_metaheader(cls, metaheader):
+        tag = re.match("^##.*=.*?[<,]ID=([^,>]*)", metaheader)
+        if tag:
+            return tag.group(1)
+        else:
+            msg = "VCF metaheader is missing ID tag [{}]"
+            raise utils.JQException(msg, metaheader)
+
     @property
     def file_name(self):
         return self._file_reader.file_name

diff --git a/test/merge_test.py b/test/merge_test.py
@@ -28,6 +28,42 @@ def __init__(self, vcf_records):
     def next_if_equals(self, dummy):
         return next(self.vcf_records_iter)
 
+class TagRegistryTestCase(test_case.JacquardBaseTestCase):
+    def test_register_tag(self):
+        registry = merge.TagRegistry()
+        actual_tag_id = registry.register_tag('DP',
+                                              '##FORMAT=<ID=DP,Descrpition="thing1">')
+        self.assertEquals("JX1_DP", actual_tag_id)
+
+        actual_tag_id = registry.register_tag('AF',
+                                              '##FORMAT=<ID=AF,Descrpition="thing1">')
+
+        self.assertEquals("JX2_AF", actual_tag_id)
+
+    def test_register_tag_returnsPreviousTagId(self):
+        registry = merge.TagRegistry()
+        actual_tag_id = registry.register_tag('DP',
+                                              '##FORMAT=<ID=DP,Descrpition="thing1">')
+        self.assertEquals("JX1_DP", actual_tag_id)
+
+        actual_tag_id = registry.register_tag('DP',
+                                              '##FORMAT=<ID=DP,Descrpition="thing1">')
+
+        self.assertEquals("JX1_DP", actual_tag_id)
+
+    def test_register_tag_passthroughJacquardTags(self):
+        registry = merge.TagRegistry()
+        actual_tag_id = registry.register_tag('JQ_AF_XX',
+                                              '##FORMAT=<ID=DP,Descrpition="thing1">')
+        self.assertEquals("JQ_AF_XX", actual_tag_id)
+
+    def test_register_tag_passthroughNonFormatTags(self):
+        registry = merge.TagRegistry()
+        actual_tag_id = registry.register_tag('FOO',
+                                              '##INFO=<ID=FOO,Descrpition="thing1">')
+        self.assertEquals("FOO", actual_tag_id)
+
+
 #TODO: rename
 class NewMergeVcfReaderTestCase(test_case.JacquardBaseTestCase):
     def setUp(self):

diff --git a/test/utils/vcf_test.py b/test/utils/vcf_test.py
@@ -622,6 +622,29 @@ def tearDown(self):
         self.output.close()
         sys.stderr = self.saved_stderr
 
+    def test_get_id_from_metaheader(self):
+        actual_id = VcfReader.get_id_from_metaheader('##FORMAT=<ID=FOO>')
+        self.assertEqual("FOO", actual_id)
+        actual_id = VcfReader.get_id_from_metaheader('##blah=<ID=FOO>')
+        self.assertEqual("FOO", actual_id)
+        actual_id = VcfReader.get_id_from_metaheader('##blah=<ID=FOO,This=That>')
+        self.assertEqual("FOO", actual_id)
+        actual_id = VcfReader.get_id_from_metaheader('##blah=<This=That,ID=FOO>')
+        self.assertEqual("FOO", actual_id)
+        actual_id = VcfReader.get_id_from_metaheader('##blah=<This=That,ID=FOO,Mine=Yours>')
+        self.assertEqual("FOO", actual_id)
+
+    def test_get_id_from_metaheader_malformedMetaheaderTakesLastId(self):
+        actual_id = VcfReader.get_id_from_metaheader('##blah=<ID=FOO,ID=BAR,ID=BAZ>')
+        self.assertEqual("BAZ", actual_id)
+
+    def test_get_id_from_metaheader_missingIdRaisesException(self):
+        metaheader = '##blah=<This=That,Mine=Yours>'
+        self.assertRaisesRegexp(utils.JQException,
+                                r"VCF metaheader is missing ID tag \[##blah=<This=That,Mine=Yours>\]",
+                                VcfReader.get_id_from_metaheader,
+                                metaheader)
+
     def test_init(self):
         file_contents = ["##metaheader1\n",
                          "##metaheader2\n",