Cleanup code

scripts/convert_tmhmm.py

@@ -10,62 +10,62 @@ parser.add_argument('--output', '-o', required=True, help='The converted results
 args = parser.parse_args()
 
 def parse_topology(s, l):
-	elements = []
-	result = []
-	flag = False
-	num = ""
-	for c in s:
-		if c == 'i' or c == 'o' or c == '-':
-			if num != "":
-				elements.append(int(num))
-				num = ""
-			if c != '-':
-				elements.append(c)
-		else:
-			num += c
-	if num != "":
-		elements.append(int(num))
-	for i in range(len(elements)):
-		if flag:
-			flag = False
-		else:
-			if elements[i] == 'i' or elements[i] == 'o':
-				location = ""
-				if elements[i] == 'i':
-					location = "inside"
-				else:
-					location = "outside"
-				if i == 0:
-					if len(elements) == 1:
-						result.append({'start': 1, 'end': l , 'location': location})
-					else:
-						result.append({'start': 1, 'end': elements[i+1]-1 , 'location': location})
-				elif i+1 == len(elements):
-					result.append({'start': elements[i-1]+1, 'end':l , 'location': location})
-				else:
-					result.append({'start': elements[i-1]+1, 'end': elements[i+1]-1 , 'location': location})
-			else:
-				result.append({'start': elements[i], 'end': elements[i+1] , 'location': 'membrane'})
-				flag = True
-	return (result)
+  elements = []
+  result = []
+  flag = False
+  num = ""
+  for c in s:
+    if c == 'i' or c == 'o' or c == '-':
+      if num != "":
+        elements.append(int(num))
+        num = ""
+      if c != '-':
+        elements.append(c)
+    else:
+      num += c
+  if num != "":
+    elements.append(int(num))
+  for i in range(len(elements)):
+    if flag:
+      flag = False
+    else:
+      if elements[i] == 'i' or elements[i] == 'o':
+        location = ""
+        if elements[i] == 'i':
+          location = "inside"
+        else:
+          location = "outside"
+        if i == 0:
+          if len(elements) == 1:
+            result.append({'start': 1, 'end': l , 'location': location})
+          else:
+            result.append({'start': 1, 'end': elements[i+1]-1 , 'location': location})
+        elif i+1 == len(elements):
+          result.append({'start': elements[i-1]+1, 'end':l , 'location': location})
+        else:
+          result.append({'start': elements[i-1]+1, 'end': elements[i+1]-1 , 'location': location})
+      else:
+        result.append({'start': elements[i], 'end': elements[i+1] , 'location': 'membrane'})
+        flag = True
+  return (result)
 
 filename = args.result
 documents = {}
 with open(filename) as f:
-	for line in f:
-		line_dic = {}
-		elements = line.rstrip().split("\t")
-		for i in range(1, len(elements)):
-			key = elements[i][:elements[i].rfind('=')]
-			value = elements[i][elements[i].rfind('=')+1:]
-			if key == 'Topology':
-				line_dic['topology'] = parse_topology(value, int(elements[i-4][elements[i-4].rfind('=')+1:]))
-			elif key == 'PredHel':
-				line_dic[key] = int(value)
-			elif not key == 'len':
-				line_dic[key] = float(value)
-		documents[elements[0]] = {'computations': [{'tool': {'name': 'TMHMM', 'version': '2.0'}, 'results': line_dic}]}
+  for line in f:
+    line_dic = {}
+    elements = line.rstrip().split("\t")
+    for i in range(1, len(elements)):
+      key = elements[i][:elements[i].rfind('=')]
+      value = elements[i][elements[i].rfind('=')+1:]
+      if key == 'Topology':
+        line_dic['topology'] = parse_topology(value, int(elements[i-4][elements[i-4].rfind('=')+1:]))
+      elif key == 'PredHel':
+        line_dic[key] = int(value)
+      elif not key == 'len':
+        line_dic[key] = float(value)
+    documents[elements[0]] = {'computations': [{'tool': {'name': 'TMHMM', 'version': '2.0'}, 'results': line_dic}]}
 
 output_filename = args.output
 with open(output_filename, 'w') as o:
-	json.dump(documents, o)
+  json.dump(documents, o)

scripts/run_tmhmm.py

@@ -9,18 +9,6 @@ tmhmm_tool = config.load_config()['tools'].get('tmhmm', 'tmhmm')
 
 parser = argparse.ArgumentParser(description='Find transmembrane helices in amino acid sequences')
 parser.add_argument('--fasta', '-f', required=True, help='A fasta file with aminoacid sequences')
-#parser.add_argument('--workdir', '-workdir', help='Working directory')
-#parser.add_argument('--wwwdir', '-wwwdir', help='The place where the www server looks for files')
-#parser.add_argument('--serverhome', '-serverhome', help='') #
-#parser.add_argument('--basedir', '-basedir', help='basis directory for TMHMM package')
-#parser.add_argument('--bindir', '-bindir', help='Bin directory (defaults basedir/bin)')
-#parser.add_argument('--scrdir', '-scrdir', help='Script directory (defaults basedir/bin)')
-#parser.add_argument('--libdir', '-libdir', help='Library directory (defaults basedir/lib)')
-#parser.add_argument('--html', '-html', help='Produce HTML output')
-#parser.add_argument('--short', '-s', help='Short output format')
-#parser.add_argument('--plot', '-p', help='Produce graphics')
-#parser.add_argument('--version1', '-v1', help='Use old model (version 1)')
-#parser.add_argument('--debugging', '-d', help='') #
 parser.add_argument('--output', required=True, help='The output file')
 args = parser.parse_args()