Merge pull request #12280 from bernt-matthias/topic/mothur-tabular

lib/galaxy/datatypes/mothur.py

@@ -494,21 +494,33 @@ class PairwiseDistanceMatrix(DistanceMatrix, Tabular):
         """
         headers = iter_headers(file_prefix, sep='\t')
         count = 0
+        names = [False, False]
         for line in headers:
-            if not line[0].startswith('@'):
-                if len(line) != 3:
-                    return False
+            if line[0].startswith('@'):
+                continue
+            if len(line) != 3:
+                return False
+            # check if col3 contains distances (floats)
+            try:
+                float(line[2])
                 try:
-                    float(line[2])
-                    try:
-                        # See if it's also an integer
-                        int(line[2])
-                    except ValueError:
-                        # At least one value is not an integer
-                        all_ints = False
+                    # See if it's also an integer
+                    int(line[2])
                 except ValueError:
-                    return False
-                count += 1
+                    # At least one value is not an integer
+                    all_ints = False
+            except ValueError:
+                return False
+            count += 1
+            # check if col1 and col2 likely contain names
+            for c in [0, 1]:
+                try:
+                    float(line[c])
+                except ValueError:
+                    names[c] = True
+
+        if not names[0] or not names[1]:
+            return False
 
         if count > 2:
             return not all_ints

lib/galaxy/datatypes/sniff.py

@@ -270,7 +270,7 @@ def guess_ext(fname, sniff_order, is_binary=False):
     >>> fname = get_test_fname('2.txt')
     >>> guess_ext(fname, sniff_order)
     'txt'
-    >>> fname = get_test_fname('2.tabular')
+    >>> fname = get_test_fname('test_tab2.tabular')
     >>> guess_ext(fname, sniff_order)
     'tabular'
     >>> fname = get_test_fname('3.txt')

lib/galaxy/datatypes/tabular.py

@@ -719,7 +719,7 @@ class Pileup(Tabular):
         >>> fname = get_test_fname( '2.txt' )
         >>> Pileup().sniff( fname )  # 2.txt
         False
-        >>> fname = get_test_fname( '2.tabular' )
+        >>> fname = get_test_fname( 'test_tab2.tabular' )
         >>> Pileup().sniff( fname )
         False
         """

lib/galaxy/datatypes/test/2.tabular

@@ -1,3 +0,0 @@
-a	2
-c	1
-d	0

lib/galaxy/datatypes/test/2.tabular

@@ -0,0 +1 @@
+../../../../test-data/2.tabular

lib/galaxy/datatypes/test/test_tab2.tabular

@@ -0,0 +1,3 @@
+a	2
+c	1
+d	0