ex-161 (jebene) initial work on metaheader sorting

umich-brcf-bioinf · Mar 30, 2015 · 8fa782f · 8fa782f
1 parent 223595d
commit 8fa782f
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diff --git a/jacquard/utils.py b/jacquard/utils.py
@@ -15,6 +15,19 @@ def round_two_digits(val):
         return val
     return val
 
+def sort_metaheaders(metaheaders):
+    metaheader_dict = {"##fileformat": 1,
+                       "##jacquard": 2,
+                       "##contig": 3,
+                       "##ALT": 4,
+                       "##FILTER": 5,
+                       "##INFO": 6,
+                       "##FORMAT": 7,
+                       "#CHROM": 8}
+
+    #pylint: disable=line-too-long
+    return sorted(metaheaders, key=lambda metaheader: metaheader_dict[metaheader.split("=")[0].split(".")[0]])
+
 class JQException(Exception):
     """Base class for all run-time exceptions in this module."""
     def __init__(self, msg, *args):

diff --git a/test/utils_test.py b/test/utils_test.py
@@ -36,6 +36,24 @@ def test_init(self):
         self.assertIsInstance(actual, Exception)
         self.assertEquals(actual.message, "msg:bar, [1, 2, 3]")
 
+class SortMetaheadersTestCase(test_case.JacquardBaseTestCase):
+    def test_sort_metaheaders(self):
+        unsorted = ["##FORMAT", "##fileformat", "##INFO", "##jacquard.foo="]
+        actual = utils.sort_metaheaders(unsorted)
+        expected = ["##fileformat", "##jacquard.foo=", "##INFO", "##FORMAT"]
+        self.assertEquals(expected, actual)
+
+    def test_sort_metaheaders_completeList(self):
+        unsorted = ["##FORMAT", "##fileformat", "##INFO", "##jacquard.foo=", "##ALT", "#CHROM", "##contig", "##FILTER"]
+        actual = utils.sort_metaheaders(unsorted)
+        expected = ["##fileformat", "##jacquard.foo=", "##contig", "##ALT", "##FILTER", "##INFO", "##FORMAT", "#CHROM"]
+        self.assertEquals(expected, actual)
+
+    def xtest_sort_metaheaders_sortsWithinCategory(self):
+        unsorted = ["##FORMAT=DP", "##FORMAT=AF", "##jacquard.bar="]
+        actual = utils.sort_metaheaders(unsorted)
+        expected = ["##jacquard.bar=", "##FORMAT=AF", "##FORMAT=DP"]
+        self.assertEquals(expected, actual)
 
 class NaturalSortTestCase(test_case.JacquardBaseTestCase):
     def test_natsort(self):