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1 from mirgene_functions import *
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2 from mirgene_graphs import *
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3 import time
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4 from multiprocessing import Process, Queue, Lock, Pool, Manager, Value
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5 import subprocess
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6 import argparse
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7
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8 subprocess.call(['mkdir','-p','split1','split2','split3','split4','Counts','Diff/temp_con','Diff/temp_tre','Diff/n_temp_con','Diff/n_temp_tre'])
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9
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10 parser = argparse.ArgumentParser()
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11 parser.add_argument("-analysis", "--anal", help="choose type of analysis", action="store")
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12 parser.add_argument("-con", "--control", help="input fastq file (controls)", nargs='+', default=[])
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13 parser.add_argument("-tre", "--treated", help="input fastq file (treated)", nargs='+', default=[] )
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14 parser.add_argument("-tool_dir", "--tool_directory", help="tool directory path", action="store")
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15 parser.add_argument("-gen", "--org_name", help="Organism", action="store")
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16 parser.add_argument("-f", "--flag", help="choose the database (MirBase,MirGene)", action="store")
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17 parser.add_argument("-percentage", "--per", help="Percentage of Samples", action="store")
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18 parser.add_argument("-counts", "--count", help="Counts for filtering", action="store")
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19 parser.add_argument("-name1", "--group1", help="Samples group 1", action="store")
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20 parser.add_argument("-name2", "--group2", help="Samples group 2", action="store")
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21 args = parser.parse_args()
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22
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23
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24 #########################################################################3###############################################################################################################################################################################################
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25
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26 if __name__ == '__main__':
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27
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28 starttime = time.time()
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29
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30 lock = Lock()
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31 manager = Manager()
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32
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33 # Download reference miRNA sequences from MirBase
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34 mature_mirnas=manager.list()
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35 ps_mature=Process(target=download_matures,args=(mature_mirnas,args.org_name))
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36 ps_mature.start()
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37
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38 # Keep the names of the files and location paths
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39 args.control[0]=args.control[0][1:]
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40 args.control[len(args.control)-1][:-1]
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41 control = [(args.control[i:i+2]) for i in range(0, len(args.control), 2)]
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42
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43 args.treated[0]=args.treated[0][1:]
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44 args.treated[len(args.treated)-1][:-1]
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45 treated = [(args.treated[i:i+2]) for i in range(0, len(args.treated), 2)]
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46
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47
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48 ############## Detection of templated isoforms ################
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49
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50 #radar = manager.list([0,0,0,0])
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51 con_samples = manager.list()
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52 con_data= manager.list()
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53 con_file_order=manager.list()
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54 con_names_seqs=manager.list()
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55 deseq=manager.list()
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56 con_unmap_seq=manager.Value('i',0)
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57 con_unmap_counts=manager.Value('i',0)
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58 con_mirna_names=manager.list()
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59 ini_con_samples = manager.list()
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60
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61 #radar1 = manager.list([0,0,0,0])
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62 tre_samples = manager.list()
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63 tre_data = manager.list()
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64 tre_file_order = manager.list()
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65 tre_names_seqs=manager.list()
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66 deseq1=manager.list()
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67 tre_unmap_seq = manager.Value('i',0)
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68 tre_unmap_counts = manager.Value('i',0)
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69 tre_mirna_names=manager.list()
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70 ini_tre_samples = manager.list()
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71
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72 # Wait for the download of reference miRNA sequences
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73 ps_mature.join()
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74 mature_mirnas=list(mature_mirnas)
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75
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76 # Processing of the detected miRNAs from SAM files
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77 ps_sam = [Process(target=sam_edit,args=(mature_mirnas,path[1][:-1],path[0].split(",")[0],"c",lock,con_samples,con_data,con_file_order,con_unmap_seq,con_names_seqs,deseq,con_mirna_names,ini_con_samples,con_unmap_counts)) for path in control]
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78 ps_sam.extend([Process(target=sam_edit,args=(mature_mirnas,path[1][:-1],path[0].split(",")[0],"t",lock,tre_samples,tre_data,tre_file_order,tre_unmap_seq,tre_names_seqs,deseq1,tre_mirna_names,ini_tre_samples,tre_unmap_counts)) for path in treated])
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79
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80 # Wait for processing of SAM files to finish
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81 [p.start() for p in ps_sam]
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82 [p.join() for p in ps_sam]
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83
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84 # Generate a histogram
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85 ps_hist=[Process(target=hist_red,args=(ini_con_samples,'c',args.group1))]
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86 ps_hist.extend([Process(target=hist_red,args=(ini_tre_samples,'t',args.group2))])
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87 [x.start() for x in ps_hist]
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88
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89 # Convert managers to lists
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90 con_samples = list(con_samples)
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91 tre_samples = list(tre_samples)
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92 con_file_order=list(con_file_order)
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93 tre_file_order=list(tre_file_order)
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94 deseq=list(deseq)
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95 deseq1=list(deseq1)
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96
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97 # Remove duplicates and sorting
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98 con_names_seqs=list(con_names_seqs)
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99 con_names_seqs.sort()
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100 con_names_seqs=list(con_names_seqs for con_names_seqs,_ in itertools.groupby(con_names_seqs))
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101
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102 tre_names_seqs=list(tre_names_seqs)
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103 tre_names_seqs.sort()
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104 tre_names_seqs=list(tre_names_seqs for tre_names_seqs,_ in itertools.groupby(tre_names_seqs))
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105
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106 # initialization of new managers
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107 new_con_file_order=manager.list()
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108 new_tre_file_order=manager.list()
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109 new_deseq=manager.list()
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110 new_deseq1=manager.list()
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111
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112 # add uncommon detected mirnas among the samples
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113 ps_un_mirnas=[Process(target=uncommon_mirnas,args=(sampp,con_names_seqs,lock,new_deseq,con_file_order[i],new_con_file_order)) for i,sampp in enumerate(deseq)]
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114 ps_un_mirnas.extend([Process(target=uncommon_mirnas,args=(sampp,tre_names_seqs,lock,new_deseq1,tre_file_order[i],new_tre_file_order)) for i,sampp in enumerate(deseq1)])
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115
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116 # Wait for processing of uncommon detected mirnas to finish
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117 [z.start() for z in ps_un_mirnas]
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118 [z.join() for z in ps_un_mirnas]
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119
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120 # Convert managers to lists
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121 new_deseq=list(new_deseq)
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122 new_deseq1=list(new_deseq1)
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123 con_file_order=list(new_con_file_order)
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124 tre_file_order=list(new_tre_file_order)
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125
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126 # Genereation of count matrices per group (controls - treated)
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127 control_group=[[x[0],x[2]] for x in new_deseq[0]]
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128 [control_group[i].append(y[i][1]) for i,_ in enumerate(control_group) for y in new_deseq]
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129
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130 treated_group=[[x[0],x[2]] for x in new_deseq1[0]]
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131 [treated_group[i].append(y[i][1]) for i,_ in enumerate(treated_group) for y in new_deseq1]
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132
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133 # Keep a copy of count matrices
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134 control_group_copy=copy.deepcopy(list(control_group))
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135 treated_group_copy=copy.deepcopy(list(treated_group))
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136
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137 # Initialization of managers
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138 merg_nam_control_group=manager.list()
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139 merg_nam_treated_group=manager.list()
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140
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141 # Merging of names different names for the same mirna sequence per group (controls, treated) to avoid duplicates
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142 ps_merge = [Process(target=merging_names,args=(control_group_copy,merg_nam_control_group))]
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143 ps_merge.extend([Process(target=merging_names,args=(treated_group_copy,merg_nam_treated_group))])
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144 [x.start() for x in ps_merge]
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145
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146 # Add unique mirna sequences between groups (all groups will have the same amount of sequences)
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147 con_list=manager.list()
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148 tre_list=manager.list()
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149
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150 ps_bw = [Process(target=black_white,args=(con_names_seqs,tre_names_seqs,treated_group,tre_list))]
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151 ps_bw.extend([Process(target=black_white,args=(tre_names_seqs,con_names_seqs,control_group,con_list))])
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152 [x.start() for x in ps_bw]
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153 [x.join() for x in ps_bw]
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154
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155 control_group=list(con_list)
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156 treated_group=list(tre_list)
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157
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158 # Detection of duplications
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159 dupes=manager.list()
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160
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161 ps_dupes = Process(target=merging_dupes,args=(control_group,dupes))
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162 ps_dupes.start()
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163 ps_dupes.join()
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164
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165 dupes=list(dupes)
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166
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167 # Merging the duplications in one entry with all different names
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168 con_list=manager.list()
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169 tre_list=manager.list()
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170
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171 ps_ap_merg_dupes = [Process(target=apply_merging_dupes,args=(control_group,dupes,con_list))]
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172 ps_ap_merg_dupes.extend([Process(target=apply_merging_dupes,args=(treated_group,dupes,tre_list))])
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173 [x.start() for x in ps_ap_merg_dupes]
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174
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175 # Preparation of reference sequences (isodforms) for the detection of non template mirnas
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176 if args.anal=="2":
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177 all_iso = manager.list()
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178 ps_non_iso = Process(target=non_template_ref,args=(con_samples,tre_samples,all_iso))
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179 ps_non_iso.start()
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180
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181 # Finishing the process for merging
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182 [x.join() for x in ps_merge]
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183 merg_nam_control_group=list(merg_nam_control_group)
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184 merg_nam_treated_group=list(merg_nam_treated_group)
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185
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186 # Export the database and the graphs
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187 procs = [Process(target=DB_write,args=(x[0],x[1],x[2],x[3],1)) for x in con_data]
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188 procs.extend([Process(target=DB_write,args=(x[0],x[1],x[2],x[3],1)) for x in tre_data])
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189 procs.extend([Process(target=make_spider,args=(merg_nam_control_group,merg_nam_treated_group,args.group1,args.group2))])
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190
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191 if args.anal == "1":
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192 procs.extend([Process(target=pie_temp,args=(merg_nam_control_group,con_unmap_seq.value,con_unmap_counts.value,merg_nam_treated_group,tre_unmap_seq.value,tre_unmap_counts.value,args.group1,args.group2))])
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193
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194 [p.start() for p in procs]
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195
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196 # Export the pdf report file
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197 if args.anal=="1":
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198 [x.join() for x in ps_hist]
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199 [p.join() for p in procs]
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200 ps_pdf = Process(target=pdf_before_DE,args=(args.anal,args.group1,args.group2))
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201 ps_pdf.start()
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202
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203 [x.join() for x in ps_ap_merg_dupes]
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204 control_group=list(con_list)
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205 treated_group=list(tre_list)
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206
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207 # Filters low count mirnas (otpional)
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208 if int(args.per)!=-1:
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209
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210 fil_con_group=manager.list()
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211 fil_tre_group=manager.list()
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212
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213 ps_low_counts = Process(target=filter_low_counts,args=(control_group,treated_group,fil_con_group,fil_tre_group,args.per,args.count))
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214 ps_low_counts.start()
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215 ps_low_counts.join()
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216
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217 fil_con_group=list(fil_con_group)
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218 fil_tre_group=list(fil_tre_group)
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219
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220 if "fil_con_group" not in locals() or "fil_con_group" not in globals():
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221 fil_con_group=control_group
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222 fil_tre_group=treated_group
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223
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224 # export count matrices
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225 ps_write = Process(target=write_main,args=(control_group, treated_group, fil_con_group, fil_tre_group, con_file_order,tre_file_order,1,args.group1,args.group2,args.per))
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226 ps_write.start()
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227
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228 # export counts files compatible with Deseq2 and EdgeR
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229 ps1_matrix = [Process(target=temp_counts_to_diff,args=(con_file_order,fil_con_group,"Diff/temp_con/",0))]
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230 ps1_matrix.extend([Process(target=temp_counts_to_diff,args=(tre_file_order,fil_tre_group,"Diff/temp_tre/",0))])
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231 [p.start() for p in ps1_matrix]
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232
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233 if args.anal=="1":
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234 ps_pdf.join()
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235 if args.anal=="2":
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236 [p.join() for p in procs]
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237 [x.join() for x in ps_hist]
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238
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239 ps_write.join()
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240 [p.join() for p in ps1_matrix]
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241
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242 ############################## Detection of Both #######################################
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243
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244 if args.anal == "2":
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245
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246 # Initialization of the managers between the proccesses
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247 # First group of samples (controls)
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248 n_con_data= manager.list()
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249 n_con_file_order=manager.list()
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250 n_con_names_seqs=manager.list()
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251 n_deseq=manager.list()
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252
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253 # Second group of samples (treated)
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254 n_tre_data = manager.list()
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255 n_tre_file_order = manager.list()
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256 n_tre_names_seqs=manager.list()
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257 n_deseq1=manager.list()
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258
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259 # Preparation of reference sequences
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260 new_ref_mirnas = list(mature_mirnas)
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261 ps_non_iso.join()
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262
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263
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264 all_iso=list(all_iso)
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265 new_ref_mirnas.extend(all_iso)
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266
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267 # Processing of non template miRNAs from SAM files
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268 ps_sam = [Process(target=non_sam_edit,args=(new_ref_mirnas,path[1][:-1],path[0].split(",")[0],"c",lock,n_con_data,n_con_file_order,n_deseq,n_con_names_seqs)) for path in control]
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269 ps_sam.extend([Process(target=non_sam_edit,args=(new_ref_mirnas,path[1][:-1],path[0].split(",")[0],"t",lock,n_tre_data,n_tre_file_order,n_deseq1,n_tre_names_seqs)) for path in treated])
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270
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271 [p.start() for p in ps_sam]
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272 [p.join() for p in ps_sam]
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273
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274 # Convert managers to lists
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275 n_con_file_order=list(n_con_file_order)
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276 n_tre_file_order=list(n_tre_file_order)
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277 n_deseq=list(n_deseq)
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278 n_deseq1=list(n_deseq1)
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279
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280 # Remove duplicates and sorting
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281 n_con_names_seqs=list(n_con_names_seqs)
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282 n_con_names_seqs.sort()
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283 n_con_names_seqs=list(n_con_names_seqs for n_con_names_seqs,_ in itertools.groupby(n_con_names_seqs))
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284
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285 n_tre_names_seqs=list(n_tre_names_seqs)
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286 n_tre_names_seqs.sort()
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287 n_tre_names_seqs=list(n_tre_names_seqs for n_tre_names_seqs,_ in itertools.groupby(n_tre_names_seqs))
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288
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289 # initialization of new managers
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290 new_n_con_file_order=manager.list()
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291 new_n_tre_file_order=manager.list()
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292 n_new_deseq=manager.list()
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293 n_new_deseq1=manager.list()
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294
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295 # add uncommon detected mirnas among the samples
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296 ps_deseq=[Process(target=uncommon_mirnas,args=(sampp,n_con_names_seqs,lock,n_new_deseq,n_con_file_order[i],new_n_con_file_order)) for i,sampp in enumerate(n_deseq)]
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297 ps_deseq.extend([Process(target=uncommon_mirnas,args=(sampp,n_tre_names_seqs,lock,n_new_deseq1,n_tre_file_order[i],new_n_tre_file_order)) for i,sampp in enumerate(n_deseq1)])
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298
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299 # Wait for processing of uncommon detected mirnas to finish
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300 [x.start() for x in ps_deseq]
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301 [x.join() for x in ps_deseq]
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302
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303 # Convert managers to lists
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304 n_new_deseq=list(n_new_deseq)
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305 n_new_deseq1=list(n_new_deseq1)
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306 n_con_file_order=list(new_n_con_file_order)
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307 n_tre_file_order=list(new_n_tre_file_order)
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308
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309 # Genereation of count matrices per group (controls - treated)
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310 n_control_group=[[x[0],x[2]] for x in n_new_deseq[0]]
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311 [n_control_group[i].append(y[i][1]) for i,_ in enumerate(n_control_group) for y in n_new_deseq]
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312
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313 n_treated_group=[[x[0],x[2]] for x in n_new_deseq1[0]]
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314 [n_treated_group[i].append(y[i][1]) for i,_ in enumerate(n_treated_group) for y in n_new_deseq1]
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315
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316 # Keep a copy of count matrices
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317 n_control_group_copy=copy.deepcopy(list(n_control_group))
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318 n_treated_group_copy=copy.deepcopy(list(n_treated_group))
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319
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320 # Initialization of managers
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321 merg_nam_n_control_group=manager.list()
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322 merg_nam_n_treated_group=manager.list()
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323
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324 # Merging of different names for the same mirna sequence per group (controls, treated) to avoid duplicates
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325 ps_merge = [Process(target=merging_names,args=(n_control_group_copy,merg_nam_n_control_group))]
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326 ps_merge.extend([Process(target=merging_names,args=(n_treated_group_copy,merg_nam_n_treated_group))])
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327 [x.start() for x in ps_merge]
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328
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329 # Add unique mirna sequences between groups (all groups will have the same amount of sequences)
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330 n_con_list=manager.list()
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331 n_tre_list=manager.list()
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332
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333 ps_bw = [Process(target=black_white,args=(n_con_names_seqs,n_tre_names_seqs,n_treated_group,n_tre_list))]
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334 ps_bw.extend([Process(target=black_white,args=(n_tre_names_seqs,n_con_names_seqs,n_control_group,n_con_list))])
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335 [x.start() for x in ps_bw]
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336 [x.join() for x in ps_bw]
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337
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338 n_control_group=list(n_con_list)
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339 n_treated_group=list(n_tre_list)
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340
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341 # Detection of duplications
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342 n_dupes=manager.list()
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343
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344 ps_dupes = Process(target=merging_dupes,args=(n_control_group,n_dupes))
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345 ps_dupes.start()
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346 ps_dupes.join()
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347
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348 n_dupes=list(n_dupes)
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349
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350 # Merging the duplications in one entry with all different names
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351 n_con_list=manager.list()
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352 n_tre_list=manager.list()
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353
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354 ps_ap_merg_dupes = [Process(target=apply_merging_dupes,args=(n_control_group,n_dupes,n_con_list))]
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355 ps_ap_merg_dupes.extend([Process(target=apply_merging_dupes,args=(n_treated_group,n_dupes,n_tre_list))])
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356 [x.start() for x in ps_ap_merg_dupes]
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357
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358 # Finishing the process for merging
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359 [x.join() for x in ps_merge]
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360 merg_nam_n_control_group=list(merg_nam_n_control_group)
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361 merg_nam_n_treated_group=list(merg_nam_n_treated_group)
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362
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363 # Export the database and the graphs
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364 procs = [Process(target=DB_write,args=(x[0],x[1],x[2],x[3],2)) for x in n_con_data]
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365 procs.extend([Process(target=DB_write,args=(x[0],x[1],x[2],x[3],2)) for x in n_tre_data])
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366 procs.extend([Process(target=logo_seq_red,args=(merg_nam_n_control_group,'c',args.group1))])
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367 procs.extend([Process(target=logo_seq_red,args=(merg_nam_n_treated_group,'t',args.group2))])
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368 procs.extend([Process(target=pie_non_temp,args=(merg_nam_control_group,merg_nam_n_control_group,merg_nam_treated_group,merg_nam_n_treated_group,con_unmap_seq.value,tre_unmap_seq.value,con_unmap_counts.value,tre_unmap_counts.value,args.group1,args.group2))])
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369
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370 [p.start() for p in procs]
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371 [p.join() for p in procs]
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372
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373 procs1 = Process(target=pdf_before_DE,args=(args.anal,args.group1,args.group2))
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374 procs1.start()
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375
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376 [x.join() for x in ps_ap_merg_dupes]
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377 n_control_group=list(n_con_list)
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378 n_treated_group=list(n_tre_list)
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379
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380 # Filters low count mirnas (otpional)
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381 if int(args.per)!=-1:
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382
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383 n_fil_con_group=manager.list()
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384 n_fil_tre_group=manager.list()
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385
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386 ps_low_counts = Process(target=filter_low_counts,args=(n_control_group,n_treated_group,n_fil_con_group,n_fil_tre_group,args.per,args.count))
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387 ps_low_counts.start()
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388 ps_low_counts.join()
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389
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390 n_fil_con_group=list(n_fil_con_group)
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391 n_fil_tre_group=list(n_fil_tre_group)
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392
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393 if "n_fil_con_group" not in locals() or "n_fil_con_group"not in globals():
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394 n_fil_con_group=n_control_group
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395 n_fil_tre_group=n_treated_group
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396
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397
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398 ps_write = Process(target=write_main,args=(n_control_group, n_treated_group,n_fil_con_group, n_fil_tre_group, n_con_file_order, n_tre_file_order,2,args.group1,args.group2,args.per))
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399 ps_write.start()
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400
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401 ps1_matrix = [Process(target=nontemp_counts_to_diff,args=(n_con_file_order,n_fil_con_group,con_file_order,fil_con_group,"Diff/n_temp_con/",0))]
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402 ps1_matrix.extend([Process(target=nontemp_counts_to_diff,args=(n_tre_file_order,n_fil_tre_group,tre_file_order,fil_tre_group,"Diff/n_temp_tre/",0))])
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403 [p.start() for p in ps1_matrix]
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404
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405 ps_write.join()
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406 [p.join() for p in ps1_matrix]
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407 procs1.join()
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28
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408 print('Running time: {} seconds'.format(round(time.time() - starttime,2)))
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4
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409
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410
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411
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412
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413
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414
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415
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416
|
