oups

bayespairing/src/parse_sequences.py

@@ -121,13 +121,13 @@ def run_fasta(input, modules_to_parse, dataset, ss="", arguments={}):
 
     if "fa" in input.lower() and ss=="":
         prediction_scores = {}
-		sequences = []
+        sequences = []
         with open(input, "rU") as f:
             for num, record in enumerate(SeqIO.parse(f, "fasta")):
                 id = record.id
                 seq = str(record.seq)
-				seq = seq.upper()
-				sequences.append(seq)
+                seq = seq.upper()
+                sequences.append(seq)
                 #print("PARSING SEQUENCE ", id, "\n")
                 if "T" in seq:
                     seq = str(seq).replace("T", "U")
@@ -176,16 +176,16 @@ def run_fasta(input, modules_to_parse, dataset, ss="", arguments={}):
 
     elif "fa" in input.lower() and ss=="infile":
         prediction_scores = {}
-		sequences = []
+        sequences = []
         with open(input, "rU") as f:
             lines = f.readlines()
             for line_n in range(0, len(lines), 3):
                 id = lines[line_n].strip(">").strip("\n")
                 seq = lines[line_n+1].strip("\n").strip()
-				seq = seq.upper()
+                seq = seq.upper()
                 ss = lines[line_n+2].strip("\n").strip()
-				sequences.append(seq)
-                p#rint("PARSING SEQUENCE ", id, "\n")
+                sequences.append(seq)
+                #print("PARSING SEQUENCE ", id, "\n")
                 if "T" in seq:
                     seq = str(seq).replace("T", "U")
                 if len(seq) <= 200:
@@ -231,9 +231,9 @@ def run_fasta(input, modules_to_parse, dataset, ss="", arguments={}):
         pickle.dump(prediction_scores,open("../output/"+o+".pickle","wb"))
     else:
         if "T" in input:
-			input = input.upper()
+            input = input.upper()
             input = str(input).replace("T", "U")
-			sequences = [input]
+            sequences = [input]
         if len(input) <= 200:
             maxs = run_BP(input, ss, modules_to_parse, dataset, "NONE", m, n, sm, mc, p, k,sscons)
             all_maxes = []