Fix lped converters and remove from flake8 blacklist

lib/galaxy/datatypes/converters/lped_to_fped_converter.py

@@ -32,49 +32,49 @@ def timenow():
 
 
 def rgConv(inpedfilepath, outhtmlname, outfilepath):
-  """convert linkage ped/map to fbat"""
-  recode = {'A': '1', 'C': '2', 'G': '3', 'T': '4', 'N': '0', '0': '0', '1': '1', '2': '2', '3': '3', '4': '4'}
-  basename = os.path.split(inpedfilepath)[-1]  # get basename
-  inmap = '%s.map' % inpedfilepath
-  inped = '%s.ped' % inpedfilepath
-  outf = '%s.ped' % basename  # note the fbat exe insists that this is the extension for the ped data
-  outfpath = os.path.join(outfilepath, outf)  # where to write the fbat format file to
-  try:
-    mf = file(inmap, 'r')
-  except:
-    sys.stderr.write('%s cannot open inmap file %s - do you have permission?\n' % (prog, inmap))
-    sys.exit(1)
-  try:
-    rsl = [x.split()[1] for x in mf]
-  except:
-      sys.stderr.write('## cannot parse %s' % inmap)
-      sys.exit(1)
-  try:
-      os.makedirs(outfilepath)
-  except:
-      pass  # already exists
-  head = ' '.join(rsl)  # list of rs numbers
-  # TODO add anno to rs but fbat will prolly barf?
-  pedf = file(inped, 'r')
-  o = file(outfpath, 'w', 2 ** 20)
-  o.write(head)
-  o.write('\n')
-  for i, row in enumerate(pedf):
-    if i == 0:
-       lrow = row.split()
-       try:
-          x = [int(x) for x in lrow[10:50]]  # look for non numeric codes
-       except:
-          dorecode = 1
-    if dorecode:
-        lrow = row.strip().split()
-        p = lrow[:6]
-        g = lrow[6:]
-        gc = [recode.get(x, '0') for x in g]
-        lrow = p + gc
-        row = '%s\n' % ' '.join(lrow)
-    o.write(row)
-  o.close()
+    """convert linkage ped/map to fbat"""
+    recode = {'A': '1', 'C': '2', 'G': '3', 'T': '4', 'N': '0', '0': '0', '1': '1', '2': '2', '3': '3', '4': '4'}
+    basename = os.path.split(inpedfilepath)[-1]  # get basename
+    inmap = '%s.map' % inpedfilepath
+    inped = '%s.ped' % inpedfilepath
+    outf = '%s.ped' % basename  # note the fbat exe insists that this is the extension for the ped data
+    outfpath = os.path.join(outfilepath, outf)  # where to write the fbat format file to
+    try:
+        mf = file(inmap, 'r')
+    except:
+        sys.stderr.write('%s cannot open inmap file %s - do you have permission?\n' % (prog, inmap))
+        sys.exit(1)
+    try:
+        rsl = [x.split()[1] for x in mf]
+    except:
+        sys.stderr.write('## cannot parse %s' % inmap)
+        sys.exit(1)
+    try:
+        os.makedirs(outfilepath)
+    except:
+        pass  # already exists
+    head = ' '.join(rsl)  # list of rs numbers
+    # TODO add anno to rs but fbat will prolly barf?
+    pedf = file(inped, 'r')
+    o = file(outfpath, 'w', 2 ** 20)
+    o.write(head)
+    o.write('\n')
+    for i, row in enumerate(pedf):
+        if i == 0:
+            lrow = row.split()
+            try:
+                x = [int(x) for x in lrow[10:50]]  # look for non numeric codes
+            except:
+                dorecode = 1
+        if dorecode:
+            lrow = row.strip().split()
+            p = lrow[:6]
+            g = lrow[6:]
+            gc = [recode.get(z, '0') for z in g]
+            lrow = p + gc
+            row = '%s\n' % ' '.join(lrow)
+        o.write(row)
+    o.close()
 
 
 def main():
@@ -108,6 +108,5 @@ def main():
     f.close()
 
 
-
 if __name__ == "__main__":
-   main()
+    main()

lib/galaxy/datatypes/converters/lped_to_pbed_converter.py

@@ -33,31 +33,31 @@ def timenow():
 
 
 def getMissval(inped=''):
-   """
-   read some lines...ugly hack - try to guess missing value
-   should be N or 0 but might be . or -
-   """
-   commonmissvals = {'N': 'N', '0': '0', 'n': 'n', '9': '9', '-': '-', '.': '.'}
-   try:
-       f = file(inped, 'r')
-   except:
-       return None  # signal no in file
-   missval = None
-   while missval == None:  # doggedly continue until we solve the mystery
+    """
+    read some lines...ugly hack - try to guess missing value
+    should be N or 0 but might be . or -
+    """
+    commonmissvals = {'N': 'N', '0': '0', 'n': 'n', '9': '9', '-': '-', '.': '.'}
+    try:
+        f = file(inped, 'r')
+    except:
+        return None  # signal no in file
+    missval = None
+    while missval is None:  # doggedly continue until we solve the mystery
         try:
-          l = f.readline()
+            l = f.readline()
         except:
-          break
+            break
         ll = l.split()[6:]  # ignore pedigree stuff
         for c in ll:
             if commonmissvals.get(c, None):
-               missval = c
-               f.close()
-               return missval
-   if not missval:
-       missval = 'N'  # punt
-   f.close()
-   return missval
+                missval = c
+                f.close()
+                return missval
+    if not missval:
+        missval = 'N'  # punt
+    f.close()
+    return missval
 
 
 def rgConv(inpedfilepath, outhtmlname, outfilepath, plink):
@@ -72,9 +72,7 @@ def rgConv(inpedfilepath, outhtmlname, outfilepath, plink):
         missval = '0'
     cl = '%s --noweb --file %s --make-bed --out %s --missing-genotype %s' % (plink, inpedfilepath, outroot, missval)
     p = subprocess.Popen(cl, shell=True, cwd=outfilepath)
-    retval = p.wait()  # run plink
-
-
+    p.wait()  # run plink
 
 
 def main():
@@ -110,6 +108,5 @@ def main():
     f.close()
 
 
-
 if __name__ == "__main__":
-   main()
+    main()