From 500a7aee64708717a187ee87b4351d1295c48a6a Mon Sep 17 00:00:00 2001
From: yhoogstrate <y.hoogstrate@gmail.com>
Date: Tue, 10 Oct 2017 11:16:09 +0200
Subject: [PATCH 1/4] test case to fix mothur.freq sniffer

---
 lib/galaxy/datatypes/mothur.py                             | 5 +++++
 .../datatypes/test/mothur_datatypetest_false_2.mothur.freq | 7 +++++++
 2 files changed, 12 insertions(+)
 create mode 100644 lib/galaxy/datatypes/test/mothur_datatypetest_false_2.mothur.freq

diff --git a/lib/galaxy/datatypes/mothur.py b/lib/galaxy/datatypes/mothur.py
index d1e016a729c..fdd462c5669 100644
--- a/lib/galaxy/datatypes/mothur.py
+++ b/lib/galaxy/datatypes/mothur.py
@@ -605,6 +605,11 @@ class Frequency(Tabular):
         >>> fname = get_test_fname( 'mothur_datatypetest_false.mothur.freq' )
         >>> Frequency().sniff( fname )
         False
+        
+        # Expression count matrix (EdgeR wrapper)
+        >>> fname = get_test_fname( 'mothur_datatypetest_false_2.mothur.freq' )
+        >>> Frequency().sniff( fname )
+        False
         """
         headers = iter_headers(filename, sep='\t')
         count = 0
diff --git a/lib/galaxy/datatypes/test/mothur_datatypetest_false_2.mothur.freq b/lib/galaxy/datatypes/test/mothur_datatypetest_false_2.mothur.freq
new file mode 100644
index 00000000000..74d16507e3a
--- /dev/null
+++ b/lib/galaxy/datatypes/test/mothur_datatypetest_false_2.mothur.freq
@@ -0,0 +1,7 @@
+GeneID	Mut1
+11287	1463
+11298	1345
+11302	5
+11303	1574
+11304	361
+11305	1762

From 787c3e575371b0969f57592a6f522d7d2634e2bc Mon Sep 17 00:00:00 2001
From: yhoogstrate <y.hoogstrate@gmail.com>
Date: Tue, 10 Oct 2017 11:55:25 +0200
Subject: [PATCH 2/4] test case to fix mothur.freq sniffer

---
 lib/galaxy/datatypes/mothur.py | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/datatypes/mothur.py b/lib/galaxy/datatypes/mothur.py
index fdd462c5669..237e857559f 100644
--- a/lib/galaxy/datatypes/mothur.py
+++ b/lib/galaxy/datatypes/mothur.py
@@ -582,6 +582,7 @@ class Oligos(Text):
 
 class Frequency(Tabular):
     file_ext = 'mothur.freq'
+    max_snif_lines = 25
 
     def __init__(self, **kwd):
         """A list of names"""
@@ -615,10 +616,11 @@ class Frequency(Tabular):
         count = 0
         for line in headers:
             if not line[0].startswith('@'):
+                # first line should be #<version string>
                 if count == 0:
-                    # first line should be #<version string>
-                    if not line[0].startswith('#') and len(line) == 1:
+                    if not line[0].startswith('#') or len(line) != 1:
                         return False
+
                 else:
                     # all other lines should be <int> <float>
                     if len(line) != 2:
@@ -626,9 +628,16 @@ class Frequency(Tabular):
                     try:
                         int(line[0])
                         float(line[1])
+
+                        if line[1].find('.') == -1:
+                            return False
                     except Exception:
                         return False
                 count += 1
+            
+            if count > self.max_snif_lines:
+                return True
+
         if count > 1:
             return True
 

From 6dd59d9d2dcf6241506cf7720729145874e66121 Mon Sep 17 00:00:00 2001
From: yhoogstrate <y.hoogstrate@gmail.com>
Date: Tue, 10 Oct 2017 13:02:10 +0200
Subject: [PATCH 3/4] flake

---
 lib/galaxy/datatypes/mothur.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/datatypes/mothur.py b/lib/galaxy/datatypes/mothur.py
index 237e857559f..349aaec436d 100644
--- a/lib/galaxy/datatypes/mothur.py
+++ b/lib/galaxy/datatypes/mothur.py
@@ -606,7 +606,7 @@ class Frequency(Tabular):
         >>> fname = get_test_fname( 'mothur_datatypetest_false.mothur.freq' )
         >>> Frequency().sniff( fname )
         False
-        
+
         # Expression count matrix (EdgeR wrapper)
         >>> fname = get_test_fname( 'mothur_datatypetest_false_2.mothur.freq' )
         >>> Frequency().sniff( fname )
@@ -634,7 +634,7 @@ class Frequency(Tabular):
                     except Exception:
                         return False
                 count += 1
-            
+
             if count > self.max_snif_lines:
                 return True
 

From 03fe2a9779dfe51659f021b6856a74cac6c44ba3 Mon Sep 17 00:00:00 2001
From: yhoogstrate <y.hoogstrate@gmail.com>
Date: Wed, 11 Oct 2017 11:29:51 +0200
Subject: [PATCH 4/4] addresses comments

---
 lib/galaxy/datatypes/mothur.py | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/lib/galaxy/datatypes/mothur.py b/lib/galaxy/datatypes/mothur.py
index 349aaec436d..c13b7d2adc9 100644
--- a/lib/galaxy/datatypes/mothur.py
+++ b/lib/galaxy/datatypes/mothur.py
@@ -582,7 +582,6 @@ class Oligos(Text):
 
 class Frequency(Tabular):
     file_ext = 'mothur.freq'
-    max_snif_lines = 25
 
     def __init__(self, **kwd):
         """A list of names"""
@@ -635,9 +634,6 @@ class Frequency(Tabular):
                         return False
                 count += 1
 
-            if count > self.max_snif_lines:
-                return True
-
         if count > 1:
             return True