changeset 29:9c0cd3b92295

Fixes for metagenomics.py datatypes tahnks to Peter Briggs

--- a/mothur/lib/galaxy/datatypes/metagenomics.py	Wed Feb 20 07:51:22 2013 -0600
+++ b/mothur/lib/galaxy/datatypes/metagenomics.py	Tue May 28 07:43:37 2013 -0500
@@ -468,23 +468,32 @@
         try:
             fh = open( filename )
             count = 0
+            line = fh.readline()
+            sequence_count = int(line.strip())
             while True:
                 line = fh.readline()
                 line = line.strip()
                 if not line:
                     break #EOF
                 if line:
-                    if line[0] != '@':
-                        linePieces = line.split('\t')
-                        if len(linePieces) != 3:
-                            return False
-                        try:
-                            check = float(linePieces[2])
-                        except ValueError:
-                            return False
-                        count += 1
-                        if count == 5:
-                            return True
+                    # Split into fields
+                    linePieces = line.split('\t')
+                    # Each line should have the same number of
+                    # fields as the Python line index
+                    linePieces = line.split('\t')
+                    if len(linePieces) != (count + 1):
+                        return False
+                    # Distances should be floats
+                    try:
+                        for linePiece in linePieces[2:]:
+                            check = float(linePiece)
+                    except ValueError:
+                        return False
+                    # Increment line counter
+                    count += 1
+                    # Only check first 5 lines
+                    if count == 5:
+                        return True
             fh.close()
             if count < 5 and count > 0:
                 return True
@@ -565,6 +574,7 @@
         try:
             fh = open( filename )
             count = 0
+            all_ints = True
             while True:
                 line = fh.readline()
                 line = line.strip()
@@ -577,14 +587,27 @@
                             return False
                         try:
                             check = float(linePieces[2])
+                            try:
+                                # See if it's also an integer
+                                check_int = int(linePieces[2])
+                            except ValueError:
+                                # At least one value is not an
+                                # integer
+                                all_ints = False
                         except ValueError:
                             return False
                         count += 1
                         if count == 5:
-                            return True
+                            if not all_ints:
+                                return True
+                            else:
+                                return False
             fh.close()
             if count < 5 and count > 0:
-                return True
+                if not all_ints:
+                    return True
+                else:
+                    return False
         except:
             pass
         finally:
@@ -910,10 +933,12 @@
                 line = line.strip()
                 if line:
                     fields = line.split('\t')
-                    if 2 <= len(fields) <= 3:
+                    if not (2 <= len(fields) <= 3):
                         return False
                     if not re.match(pat,fields[1]):
                         return False
+                    if len(fields) == 3:
+                        check = int(fields[2])
                     count += 1
                     if count > 10:
                         break
@@ -1117,6 +1142,9 @@
                     fields = line.split('\t')
                     if col_cnt == None:  # ignore values in first line as they may be column headings
                         col_cnt = len(fields)
+                        # There should be at least 2 columns
+                        if col_cnt < 2:
+                            return False
                     else:  
                         if len(fields) != col_cnt :
                             return False