rework to use python3

NullDistEstimation/1_renormAll.py

@@ -1,24 +1,27 @@
-#!/usr/bin/python
+#!/usr/bin/env python3
 # Usage: "python 1_renormAll.py %s %s %s %s" % (contraList, renormPath, renormList, debug)
 
 import math
 import os
 import sys
 
 if len(sys.argv) < 5:
-    print "Error: 1_renormAll.py Not enough arguments"
+    print("Error: 1_renormAll.py Not enough arguments")
     sys.exit(0)
 
 contraList = sys.argv[1]
 renormPath = sys.argv[2]
 renormList = sys.argv[3]
 debug = sys.argv[4]
 
-if debug == 'T':
-    a_and_b = open(os.path.join(os.path.split(renormList)[0],'debug/1_abstats.txt'), 'w')
-    a_and_b.write('SampleName\ta_2\tb_2\t\n')
+if debug == "T":
+    a_and_b = open(
+        os.path.join(os.path.split(renormList)[0], "debug/1_abstats.txt"), "w"
+    )
+    a_and_b.write("SampleName\ta_2\tb_2\t\n")
 
-def renorm_file(path_CONTRA_out, path_out): # Arguments: two paths to files
+
+def renorm_file(path_CONTRA_out, path_out):  # Arguments: two paths to files
     f_CONTRA_out = open(path_CONTRA_out, "r")
     f_out = open(path_out, "w")
 
@@ -29,23 +32,24 @@ def renorm_file(path_CONTRA_out, path_out): # Arguments: two paths to files
     headers = lines[0]
     contra = []
     for line in lines[1:]:
-        contra.append(line.split('\t'))
+        contra.append(line.split("\t"))
     # For each line in contra:
     # 0 = region ID, 6 = Mean.of.LogRatio, 7 = Adjusted.Mean.of.LogRatio, 14 = tumour.rd, 15 = normal.rd, 16 = tumour.rd.ori, 17 = normal.rd.ori
-        
+
     # 2. Go through data, calculating x_T, N_T, x_N, N_N
     # as well as creating list of genes to remove (big gains)
-    removed_regions = [] # Listed by region ID
-    remove_threshold = 2 # Arbitrarily chosen - can be adjusted
+    removed_regions = []  # Listed by region ID
+    remove_threshold = 2  # Arbitrarily chosen - can be adjusted
     ##### PROBLEM: due to threshold might only take some regions of a particular gene when in reality, want all of them??
     # Does this make a difference?
     x_T = N_T = x_N = N_N = 0.0
 
     # 4 = OriStCoordinate, 5 = OriEndCoordinate
 
-
     for line in contra:
-        k = float(line[5]) - float(line[4]) + 1 # Width / number of bases. Inclusive, so add 1.
+        k = (
+            float(line[5]) - float(line[4]) + 1
+        )  # Width / number of bases. Inclusive, so add 1.
         if float(line[7]) > remove_threshold:
             removed_regions.append(line[0])
             x_T += float(line[16]) * k
@@ -56,42 +60,47 @@ def renorm_file(path_CONTRA_out, path_out): # Arguments: two paths to files
     # print removed_regions
 
     # 3. Calculate a_2, b_2
-    n = 1 - float(x_N)/N_N
-    t = 1 - float(x_T)/N_T
-    a_2 = math.sqrt(n/t)
-    b_2 = math.sqrt(t/n) # or 1/a_2
-
+    n = 1 - float(x_N) / N_N
+    t = 1 - float(x_T) / N_T
+    a_2 = math.sqrt(n / t)
+    b_2 = math.sqrt(t / n)  # or 1/a_2
 
     # 4. Rescale read depths (and recalculate log ratio??)
     # Add to new columns
     # Need to multiply necessary tumour.rd (d_t) by a_2, normal.rd (d_n) by b_2
-    headers = "Gene.Sym\tChr\tOriStCoordinate\tOriEndCoordinate\tMean.of.Log.Ratio.readj\n" # fix headers
+    headers = (
+        "Gene.Sym\tChr\tOriStCoordinate\tOriEndCoordinate\tMean.of.Log.Ratio.readj\n"
+    )  # fix headers
     f_out.write(headers)
     for line in contra:
         temp = [line[2], line[3], line[4], line[5]]
         # calculate new read depths (actually you dont need these)
-        #temp.append(str(float(line[14]) * a_2))
-        #temp.append(str(float(line[15]) * b_2))
+        # temp.append(str(float(line[14]) * a_2))
+        # temp.append(str(float(line[15]) * b_2))
         # Recalculate Mean.of.Log.Ratio
-        temp.append(str(math.log((float(line[14]) * a_2) /(float(line[15]) * b_2 ), 2))+'\n')
+        temp.append(
+            str(math.log((float(line[14]) * a_2) / (float(line[15]) * b_2), 2)) + "\n"
+        )
         # Write to output
-        f_out.write('\t'.join(temp))
+        f_out.write("\t".join(temp))
 
     # 5. Close file
     f_out.close()
 
-    if debug == 'T':
-        a_and_b.write('\t'.join([os.path.basename(path_CONTRA_out), str(a_2), str(b_2)+'\n']))
+    if debug == "T":
+        a_and_b.write(
+            "\t".join([os.path.basename(path_CONTRA_out), str(a_2), str(b_2) + "\n"])
+        )
 
 
 # get file paths from list
 # note that these are paths, not just names: makes it a bit trickier
-dirs = open(contraList, 'r')
-renormGood = open(renormList, 'w')
+dirs = open(contraList, "r")
+renormGood = open(renormList, "w")
 filepaths = []
 bad_filepaths = []
 for line in dirs.readlines():
-    filepaths.append(line.rstrip('\n\r'))
+    filepaths.append(line.rstrip("\n\r"))
 dirs.close()
 
 middle = "/table/"
@@ -102,21 +111,20 @@ def renorm_file(path_CONTRA_out, path_out): # Arguments: two paths to files
 count = 0
 for filepath in filepaths:
     count += 1
-    if count % 100 == 0 and debug == 'T':
-        print "...Now processing "+str(count)+"..."
-    filename = os.path.basename(filepath.rstrip("/\\ ")) # want to get file
-    cfilepath = os.path.join(filepath+middle, filename+suffix)
+    if count % 100 == 0 and debug == "T":
+        print(f"...Now processing {str(count)}...")
+    filename = os.path.basename(filepath.rstrip("/\\ "))  # want to get file
+    cfilepath = os.path.join(filepath + middle, filename + suffix)
     # print cfilepath
-    outpath = os.path.join(renormPath, filename+outsuffix)
+    outpath = os.path.join(renormPath, filename + outsuffix)
     if os.path.exists(cfilepath):
         renorm_file(cfilepath, outpath)
-        renormGood.write(filename+'\n')
+        renormGood.write(filename + "\n")
     else:
         bad_filepaths.append(filename)
 
-if debug == 'T':
+if debug == "T":
     a_and_b.close()
-    print "Finished processing out to %s" % renormList
-    print "Bad paths:"
-    print " ".join(bad_filepaths)
-
+    print(f"Finished processing out to {renormList}")
+    print("Bad paths:")
+    print(" ".join(bad_filepaths))