LSA soft clustering

+import os
+from optparse import OptionParser
+import sys
+from time import time
+import re
+import numpy as np
+
+# Objective: Obtain groups according to the component with the higher absolute value
+
+# Parameters:
+#   1) --vectorPath Path to read vectors.
+#   2) --vectorFile File to read vectors.
+#   3) --outputPath Path to place output files.
+#   4) --groups Number of groups
+
+# Ouput:
+#   1) File with groups and plots
+
+# Execution:
+# python plot_Vectors_LSA_structured_heatmap.py --outputPath /home/compu2/bionlp/lcg-faaa/agrupamiento-datos-categoricos --vectorPath /home/compu2/bionlp/lcg-faaa/agrupamiento-datos-categoricos --vectorFile vectors_file.txt --groups 2
+
+###########################################################
+#                       MAIN PROGRAM                      #
+###########################################################
+
+def getGroup(v):
+    if np.max(v) == 0:
+        index_max = len(v)
+    else:
+        index_max = np.argmax(v)
+    return index_max
+
+def getGroupSign(v):
+    sign = ''
+    vabs = [abs(i) for i in v]
+    if np.max(vabs) == 0:
+        index_max = len(vabs)
+        sign = '(+/-)'
+    else:
+        index_max = np.argmax(vabs)
+        sign = '(' + str(v[index_max])[:5] + ')'
+    return index_max, sign
+
+if __name__ == "__main__":
+    # Parameter definition
+    parser = OptionParser()
+    parser.add_option("--vectorPath", dest="vectorPath",
+                      help="Path to read vector file", metavar="PATH")
+    parser.add_option("--vectorFile", dest="vectorFile",
+                      help="File to read vectors", metavar="FILE")
+    parser.add_option("--outputPath", dest="outputPath",
+                      help="Path to place clustering classified files", metavar="PATH")
+    parser.add_option("--groups", type="int",
+                      dest="groups", default=0,
+                      help="Groups", metavar="N")
+
+    (options, args) = parser.parse_args()
+    if len(args) > 0:
+        parser.error("None parameters indicated.")
+        sys.exit(1)
+
+    # Printing parameter values
+    print('-------------------------------- PARAMETERS --------------------------------')
+    print("Path to read vector file: " + str(options.vectorPath))
+    print("File to read vectors: " + str(options.vectorFile))
+    print("Output path: " + str(options.outputPath))
+    print("Groups:" + str(options.groups))
+
+    listVectors = []
+    listLabels = []
+    listGroup = []
+    vectorLen = int(options.groups)
+    t0 = time()
+    with open(os.path.join(options.vectorPath, options.vectorFile), mode="r", encoding='utf8') as iFile:
+        for line in iFile.readlines():
+            if line.startswith("#"):
+                continue
+            line = line.strip('\r\n')
+            listLine = line.split('\t')
+            label = listLine[0]
+            vector = []
+            vectorOrig = []
+            listValues = listLine[1].split()
+            if len(listValues) != vectorLen:
+                print("Vector vectorLen does not match: {}".format(label))
+                continue
+            for elem in listValues:
+                vectorOrig.append(float(elem))
+                vector.append(abs(float(elem)))
+            listVectors.append(vector)
+            #group = getGroupSign(vectorOrig)
+            group = getGroup(vectorOrig)
+            listGroup.append(group[0])
+            #listSign.append(group[1])
+            listLabels.append(label + group[1])
+    print("   Reading vectors done!")
+    print("    Len vectors: " + str(len(listVectors)))
+    print("    Len labels: " + str(len(listLabels)))
+
+    with open(os.path.join(options.outputPath, options.vectorFile.replace('.txt', '.grps.txt')), mode='w', encoding='utf8') as oFile:
+        for g, l in sorted(zip(listGroup, listLabels)):
+            oFile.write('{}\t{}\n'.format(g, l))
+
+    with open(os.path.join(options.outputPath, options.vectorFile.replace('.txt', '.grps-rows.txt')), mode='w', encoding='utf8') as oFile:
+        g_before = 0
+        labels = ''
+        for g, l in sorted(zip(listGroup, listLabels)):
+            if g != g_before:
+                oFile.write('{}\t{}\n'.format(g_before, labels.rstrip(', ')))
+                labels = ''
+                g_before = g
+            labels = labels + l + ', '
+        oFile.write('{}\t{}\n'.format(g_before, labels.rstrip(', ')))
+
+    print("   Processing done in %fs" % (time() - t0))