minor cleanup

alleles_generator/seqInfo.py

@@ -1,6 +1,5 @@
 from bitarray import bitarray
 
-from main_tools.my_random import MY_RANDOM as random
 from main_tools.housekeeping import debugPrint
 
 
@@ -23,7 +22,7 @@ def __repr__(self):
         return self.name
 
 
-def create_sequences(processedData, args):
+def create_sequences(processedData):
     '''
     Parameters: args is a dictionary that maps the SNP file to 
     array_template

ascertainment/pseudo_array.py

@@ -35,7 +35,7 @@ def find2(a, x):
         elif d1==d2:
             return i
 
-def add_snps(avail_sites, nb_avail_sites, pos_asc, nbss_asc, nb_array_snps):
+def add_snps(avail_sites, nb_avail_sites, pos_asc, nbss_asc):
     ''''
     This function is called 199 times when the program is 
     ran. 
@@ -149,7 +149,7 @@ def pseudo_array(asc_panel, daf, pos, snps):
             diff = int(len(snps) - len(pos_asc))
             for m in range(1, diff + 1):
                 pos_asc2 = []
-                pos_asc2 = add_snps(avail_sites, nb_avail_sites, pos_asc, nbss_asc, nb_array_snps)
+                pos_asc2 = add_snps(avail_sites, nb_avail_sites, pos_asc, nbss_asc)
                 pos_asc = pos_asc2
                 nbss_asc = len(pos_asc)
                 if nbss_asc == len(snps):
@@ -266,7 +266,7 @@ def pseudo_array_bits(asc_panel_bits, daf, pos, snps):
             diff = int(len(snps) - len(pos_asc))
             for m in range(1, diff + 1):
                 pos_asc2 = []
-                pos_asc2 = add_snps(avail_sites, nb_avail_sites, pos_asc, nbss_asc, nb_array_snps)
+                pos_asc2 = add_snps(avail_sites, nb_avail_sites, pos_asc, nbss_asc)
                 pos_asc = pos_asc2
                 nbss_asc = len(pos_asc)
                 if nbss_asc == len(snps):

main_tools/write_files.py

@@ -1,11 +1,11 @@
 import os
 
 def create_sim_directories(path_name):
-    '''
-    Parameter: pathname, which is currently output_dir
-
-    Returns: dir_list (['output_dir/sim_data', 'output_dir/germline_out', 'output_dir/results'])
-    '''
+    """
+    
+    :param path_name: which is currently output_dir
+    :return: dir_list (['output_dir/sim_data', 'output_dir/germline_out', 'output_dir/results'])
+    """
     sim_data_dir     = str(path_name)+'/sim_data'
     germline_out_dir = str(path_name)+'/germline_out'
     sim_results_dir  = str(path_name)+'/results'
@@ -22,24 +22,25 @@ def create_sim_directories(path_name):
 
 
 def write_sim_results_file(dir, job, param_dict, res_list, header):
-    '''
-    Parameters:
-    dir = output_dir/results
-    job = 1
-    param_dict = {'A': '44499.7180488', 'daf': '0.0264139586625', 'B': '40008.4616861', 'AB_t': '2546.95287896', 'AN': '10000.0', 'AN_t': '2113.43905612'}
-    res_list = [4372, 1724, 590, -0.40890634648504526, 165, 27, 11, 57.40526315789474, 0.970678370998841, 158, 4, 1, 49.15632065775952, 2.3175661604382545, 0.03793034448167276]
-    header = ['SegS_D1_CGI', 'Sing_D1_CGI', 'Dupl_D1_CGI', 'TajD_D1_CGI', 'SegS_D1_ASC', 'Sing_D1_ASC', 'Dupl_D1_ASC', 'Pi_D1_ASC', 'TajD_D1_ASC', 'SegS_S1_ASC', 'Sing_S1_ASC', 'Dupl_S1_ASC', 'Pi_S1_ASC', 'TajD_S1_ASC', 'FST_D1_S1_ASC']
-    '''
+    """
+    
+    :param dir: output_dir/results
+    :param job: 1
+    :param param_dict: {'A': '44499.7180488', 'daf': '0.0264139586625', 'B': '40008.4616861', 'AB_t': '2546.95287896', 'AN': '10000.0', 'AN_t': '2113.43905612'}
+
+    :param res_list: [4372, 1724, 590, -0.40890634648504526, 165, 27, 11, 57.40526315789474, 0.970678370998841, 158, 4, 1, 49.15632065775952, 2.3175661604382545, 0.03793034448167276] 
+    :param header: ['SegS_D1_CGI', 'Sing_D1_CGI', 'Dupl_D1_CGI', 'TajD_D1_CGI', 'SegS_D1_ASC', 'Sing_D1_ASC', 'Dupl_D1_ASC', 'Pi_D1_ASC', 'TajD_D1_ASC', 'SegS_S1_ASC', 'Sing_S1_ASC', 'Dupl_S1_ASC', 'Pi_S1_ASC', 'TajD_S1_ASC', 'FST_D1_S1_ASC']
+    :return: 
+    """
+
     result = '{}/results_{}.txt'.format(dir, job)
     out_file = open(result, 'w')
 
-    #lines write_sims_file
     params = []
     vals = []
     for param, val in param_dict.items():
         params.append(param)
         vals.append(str(val))
-    #header from write_results_file
     header = '\t'.join(header)+'\n'
     out = '\t'.join([str(r) for r in res_list]) + '\n'
 

real_data_ss.py

@@ -59,7 +59,7 @@ def main(args):
         using_pseudo_array = False
 
     ### Create a list of Sequence class instances. These will contain the bulk of all sequence-based data
-    sequences = create_sequences(processedData, args)
+    sequences = create_sequences(processedData)
     names = [seq.name for seq in sequences]
 
     n_d = sum([1 for seq in sequences if seq.type == 'discovery'])

simprily.py

@@ -46,7 +46,7 @@ def main(args):
 
 
     ### Create a list of Sequence class instances. These will contain the bulk of all sequence-based data
-    sequences = create_sequences(processedData, args)
+    sequences = create_sequences(processedData)
     names = [seq.name for seq in sequences]
 
     n_d = sum([1 for seq in sequences if seq.type == 'discovery'])

simulation/run_sim.py

@@ -4,22 +4,19 @@
 
 
 def run_macs(macs_args, sequences):
-    '''
-    Parameters: sequences and macs_args
-    macs_args:
-    ['./bin/macs', '166.0', '1000000', '-I', '2', '26', '140',
+    """
+    :param macs_args:     ['./bin/macs', '166.0', '1000000', '-I', '2', '26', '140',
      '-t', '0.00444997180488', '-s', '1231', '-r', '0.00177998872195', 
      '-h', '1e5', '-n', '1', '1.0', '-n', '2', '0.899072251249', '-en',
     '0.0118708617304', '1', '0.224720524949', '-ej', '0.0143090794261',
      '2', '1', '-R', 'genetic_map_b37/genetic_map_GRCh37_chr1.txt.macshs']
-
-    sequences: [A, B], which is a sequence type
-
-    Returns: sequences, which is a list of two instance types stored as 
+    :param sequences: [A, B], which is a sequence type
+    :return: sequences, which is a list of two instance types stored as 
     [A, B]
     position: list of floats cast as strings, length: 10752
     the floaty strings increase from '0.000178136752' to '     0.99995896'
-    '''
+    """
+
     debugPrint(2,"running macs simulation:")
     position = []
     null = open(os.devnull, 'w')
@@ -42,8 +39,5 @@ def run_macs(macs_args, sequences):
             #     debugPrint(3,line)
         else:
             break
-   # print("THIS IS SEQUENCES zero: " + str(sequences[0].__dict__))
-   # print("THIS IS SEQUENCES one: " + str(sequences[1].__dict__))
-   # print("THIS IS position:  " + str(position))
  #   debugPrint(2,"Finished macs simulation")
     return [sequences,position]

summary_statistics/germline_tools.py

@@ -1,7 +1,6 @@
 from subprocess import Popen
 
 def run_germline(ped_name, map_name, out_name, min_m):
-    print("THIS IS THE ")
     print( 'Running Germline on ' + ped_name + ' ' + map_name)
 
     bash_command = 'bash ./bin/phasing_pipeline/gline.sh ./bin/germline-1-5-1/germline  {0} {1} {2} "-bits 10 -min_m {3}"'.format(

unit_test.py

@@ -274,23 +274,23 @@ def test_add_snps(self):
         pos_asc = [3000, 3000, 3000]
         nbss_acs  = 198
         nb_array_snps = 200
-        check = add_snps(avail_sites, nb_avail_sites, pos_asc, nbss_acs, nb_array_snps)
+        check = add_snps(avail_sites, nb_avail_sites, pos_asc, nbss_acs)
         self.assertEquals(check, [3000, 3000, 3000])
 
         avail_sites = [1.0, 2.0]
         nb_avail_sites = 1000
         pos_asc = [12, 12, 12]
         nbss_acs = 23
         nb_array_snps = 200
-        check = add_snps(avail_sites, nb_avail_sites, pos_asc, nbss_acs, nb_array_snps)
+        check = add_snps(avail_sites, nb_avail_sites, pos_asc, nbss_acs)
         self.assertEquals(check, [12, 12 ,12])
 
         avail_sites = [21313211242134]
         nb_avail_sites = 3000
         pos_asc = [-1, -1, 3000]
         nbss_acs  = 23
         nb_array_snps = 200
-        check = add_snps(avail_sites, nb_avail_sites, pos_asc, nbss_acs, nb_array_snps)
+        check = add_snps(avail_sites, nb_avail_sites, pos_asc, nbss_acs)
         self.assertEquals(check, [-1, -1, 3000])
 
         # this one is defined
@@ -299,7 +299,7 @@ def test_add_snps(self):
         pos_asc = [12, -1, 2]
         nbss_acs  = 23
         nb_array_snps = 200
-        check = add_snps(avail_sites, nb_avail_sites, pos_asc, nbss_acs, nb_array_snps)
+        check = add_snps(avail_sites, nb_avail_sites, pos_asc, nbss_acs)
         self.assertEquals(check, [12, -1, 2, 3])
 
         # defined, even though nbss_acs is negative and a float
@@ -308,7 +308,7 @@ def test_add_snps(self):
         pos_asc = [12, -1, 2]
         nbss_acs  = -1
         nb_array_snps = 200
-        check = add_snps(avail_sites, nb_avail_sites, pos_asc, nbss_acs, nb_array_snps)
+        check = add_snps(avail_sites, nb_avail_sites, pos_asc, nbss_acs)
         self.assertEquals(check, [12, -1, 2, 3])
 
         # not defined
@@ -317,7 +317,7 @@ def test_add_snps(self):
         pos_asc = [12, 8000001, 2]
         nbss_acs  = -1
         nb_array_snps = 200
-        check = add_snps(avail_sites, nb_avail_sites, pos_asc, nbss_acs, nb_array_snps)
+        check = add_snps(avail_sites, nb_avail_sites, pos_asc, nbss_acs)
         self.assertEquals(check, [12, 8000001, 2])
 
         '''