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1 import itertools
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2 import re
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3 import urllib.request
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4 import gzip
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5 import copy
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6 from collections import OrderedDict
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7
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8
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9
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10 # Read a file and return it as a list
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11 def read(path, flag):
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12 if flag == 0:
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13 with open(path) as fp:
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14 file=fp.readlines()
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15 fp.close()
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16 return file
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17
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18 if flag == 1:
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19 with open(path) as fp:
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20 file = fp.read().splitlines()
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21 fp.close()
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22 return file
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23
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24 # Write a list to a txt file
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25 def write(path, list):
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26 with open(path,'w') as fp:
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27 for x in list:
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28 fp.write(str("\t".join(x[1:-1])))
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29 fp.close()
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30
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31
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32 #################################################################################################################>
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33
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34 # Detect the longest common substring sequence between two mirnas
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35 def longestSubstring(str1, str2):
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36
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37 from difflib import SequenceMatcher
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38 # initialize SequenceMatcher object with
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39 # input string
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40 seqMatch = SequenceMatcher(None, str1, str2)
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41
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42 # find match of longest sub-string
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43 # output will be like Match(a=0, b=0, size=5)
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44 match = seqMatch.find_longest_match(0, len(str1), 0, len(str2))
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45
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46 # print longest substring
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47 if (match.size != 0):
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48 return str1[match.a: match.a + match.size]
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49 else:
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50 print('No longest common sub-string found')
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51
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52 #################################################################################################################################################################################################################
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53
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54 """
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55
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56 This function concatenates miRNAs which are generated from different chromosomes
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57 and eliminates the duplications of miRNAs on every sample
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58
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59 input: detected miRNAs
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60 output: collpased miRNAs without duplicates
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61
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62 """
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63
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64
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65 def remove_duplicates(mirnas):
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66
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67 # Detection of canonical mirRNAs whicha are generated from different chromosomes
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68 dupes=[[x[9],x[0],x[2]] for x in mirnas]
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69
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70 for x in mirnas:
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71 for y in dupes:
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72 if x[9] == y[0] and x[0] == y[1] and x[2].split("_")[0] == y[2].split("_")[0] and x[2] != y[2]:
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73 y.append(x[2])
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74
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75 # Detection of different chromosomes for every miRNA
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76 chr_order = []
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77 for x in dupes:
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78 temp = []
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79 for i in range(2,len(x)):
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80 if x[i].split("chr")[1].split("(")[0].isdigit():
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81 temp.append(int(x[i].split("chr")[1].split("(")[1][0]+x[i].split("chr")[1].split("(")[0]))
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82 else:
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83 temp.append(x[i].split("chr")[1][0:4])
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84
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85 for z in temp:
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86 if 'X(-)'==z or 'Y(-)'==z or 'X(+)'==z or 'Y(+)'==z:
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87 temp = [str(j) for j in temp]
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88 temp = list(set(temp))
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89 temp.sort()
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90 chr_order.append(temp)
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91
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92 # Collapsing the miRNAs with the same sequence from different chromosomes
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93 collapsed_dupes=[]
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94 for i in range(len(dupes)):
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95 collapsed_dupes.append([dupes[i][0],dupes[i][2].split("_")[0],dupes[i][1]])
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96 for x in chr_order[i]:
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97 chr_check = re.match("[-+]?\d+$", str(x)) # check if chromosome is 'X' or 'Y'
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98 if chr_check is not None:
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99 if int(x)<0: # Check the strand (+) or (-)
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100 collapsed_dupes[i][1]= collapsed_dupes[i][1]+"_chr"+str(abs(int(x)))+"(-)"
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101 else:
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102 collapsed_dupes[i][1] = collapsed_dupes[i][1] + "_chr" + str(abs(int(x)))+"(+)"
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103 else:
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104 collapsed_dupes[i][1] = collapsed_dupes[i][1] + "_chr" + str(x)
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105
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106 # Remove duplicates from collapsed_dupes
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107 collapsed_dupes.sort()
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108 collapsed_dupes = list(collapsed_dupes for collapsed_dupes,_ in itertools.groupby(collapsed_dupes))
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109
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110 for i in range(len(mirnas)):
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111 for x in collapsed_dupes:
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112
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113 # Naming of template isomirs (adding positions in the names)
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114 if mirnas[i][9] == x[0] and mirnas[i][0] == x[2] and len(mirnas[i][2].split("_")) >3 and mirnas[i][2].split("_")[0]==x[1].split("_")[0]:
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115 gg=str("_t_"+mirnas[i][2].split("_")[-2]+"_"+mirnas[i][2].split("_")[-1])
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116 mirnas[i][2] = x[1]+gg
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117 break
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118
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119 # Naming of canonical miRNAs (collpsed names)
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120 if mirnas[i][9]==x[0] and mirnas[i][0]== x[2] and len(mirnas[i][2].split("_"))==3 and mirnas[i][2].split("_")[0]==x[1].split("_")[0]:
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121 mirnas[i][2] = x[1]
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122 break
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123
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124 # Remove duplicates
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125 mirnas.sort()
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126 mirnas=list(mirnas for mirnas,_ in itertools.groupby(mirnas))
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127
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128 return mirnas
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129
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130 #############################################################################################################################################################################################################
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131
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132 """
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133
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134 This function indentifies and classifies the miRNAs which are detected from the alignment tool.
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135
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136 """
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137
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138 def sam_edit(mature_mirnas,path,file,case,l,samples,data,file_order,unmap_seq,names_n_seqs,deseq,mirna_names,ini_sample,unmap_counts):
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139
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140 # read the sam file
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141 ini_sam=read(path,0)
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142 main_sam = [x.rstrip("\n").split("\t") for x in ini_sam if "@" not in x.split("\t")[0]] # remove introduction
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143 unique_seq = [x for x in main_sam if x[1] == '0' and len(x[9])>=18 and len(x[9])<=26] # keeps only the functional miRNAs
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144 filter_sam = [[x[0],x[1],x[2],len(x[9])] for x in main_sam] # keeps only the necessary info of miRNAs from sam files (name, sequence, counts, etc)
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145
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146 sorted_uni_arms = []
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147
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148 for i in range(0,len(mature_mirnas,),2):
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149 tmp_count_reads = 0 # calculate the total number of reads
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150 tmp_count_seq = 0 # calculate the total number of sequences
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151 for j in range(len(unique_seq)):
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152
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153 if "{" in unique_seq[j][2].split("_")[0]: # checks if a miRNA is generated from two different locis on the same chromosome
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154 mirna=unique_seq[j][2].split("_")[0][:-4]
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155 else:
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156 mirna=unique_seq[j][2].split("_")[0]
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157
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158 # Detection of differences between the canonical miRNA and the detected miRNA
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159 if mature_mirnas[i].split(" ")[0][1:] == mirna:
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160
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161 temp_mature = mature_mirnas[i+1].strip().replace("U", "T")
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162 off_part = longestSubstring(temp_mature, unique_seq[j][9])
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163
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164 mat_diff = temp_mature.split(off_part)
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165 mat_diff = [len(mat_diff[0]), len(mat_diff[1])]
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166
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167 unique_diff = unique_seq[j][9].split(off_part)
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168 unique_diff = [len(unique_diff[0]), len(unique_diff[1])]
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169
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170 # Handling of some special mirnas like (hsa-miR-8485)
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171 if mat_diff[1]!=0 and unique_diff[1]!=0:
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172 unique_seq[j]=1
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173 pre_pos = 0
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174 post_pos = 0
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175
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176 elif mat_diff[0]!=0 and unique_diff[0]!=0:
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177 unique_seq[j]=1
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178 pre_pos = 0
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179 post_pos = 0
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180
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181 else:
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182 # Keep the findings
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183 pre_pos = mat_diff[0]-unique_diff[0]
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184 post_pos = unique_diff[1]-mat_diff[1]
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185 tmp_count_reads = tmp_count_reads + int(unique_seq[j][0].split("-")[1])
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186 tmp_count_seq = tmp_count_seq+1
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187
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188 # Store the detected miRNAs with new names according to the findings
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189 if pre_pos != 0 or post_pos != 0:
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190 if pre_pos == 0:
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191 unique_seq[j][2] = unique_seq[j][2].split("_")[0]+"_"+unique_seq[j][2].split("_")[2]+ "_t_" +str(pre_pos) + "_" + '{:+d}'.format(post_pos)
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192 elif post_pos == 0:
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193 unique_seq[j][2] = unique_seq[j][2].split("_")[0]+"_"+unique_seq[j][2].split("_")[2] + "_t_" + '{:+d}'.format(pre_pos) + "_" + str(post_pos)
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194 else:
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195 unique_seq[j][2] = unique_seq[j][2].split("_")[0]+"_"+unique_seq[j][2].split("_")[2]+"_t_"+'{:+d}'.format(pre_pos)+"_"+'{:+d}'.format(post_pos)
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196
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197 # Remove the values "1" from the handling of special mirnas (hsa-miR-8485)
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198 for x in range(unique_seq.count(1)):
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199 unique_seq.remove(1)
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200
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201 # metrics for the production of database
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202 if tmp_count_reads != 0 and tmp_count_seq != 0:
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203 sorted_uni_arms.append([mature_mirnas[i].split(" ")[0][1:], tmp_count_seq, tmp_count_reads])
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204
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205 # Sorting of the metrics for database
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206 sorted_uni_arms = sorted(sorted_uni_arms, key=lambda x: x[1], reverse=True)
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207
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208 # Collapsing of miRNAs and removing of duplicates
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209 collapsed_mirnas = remove_duplicates(unique_seq)
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210
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211 # Correction of metrics due to the collapsing and removing of duplicates for the production of Database
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212 for y in sorted_uni_arms:
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213 counts=0
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214 seqs=0
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215 for x in collapsed_mirnas:
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33
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216 if y[0] in x[2].split("_")[0]:
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217 counts+=int(x[0].split("-")[1])
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218 seqs+=1
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219
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220 y[1]=seqs
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221 y[2]=counts
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222
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223
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224 # Output variables
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225 temp_mirna_names=[]
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226
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227 l.acquire()
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228
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229 if case == "c" or case == "t":
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230 temp_mirna_names.extend(z[2] for z in collapsed_mirnas)
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231 names_n_seqs.extend([[y[2],y[9]] for y in collapsed_mirnas])
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232 deseq.append([[x[2], x[0].split('-')[1], x[9]] for x in collapsed_mirnas])
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233 mirna_names.extend(temp_mirna_names)
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234 unmap_seq.value += sum([1 for x in main_sam if x[1] == '4']) # Keeps the unmap unique sequences for the production of a graph
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235 unmap_counts.value += sum([int(x[0].split("-")[1]) for x in main_sam if x[1] == '4']) # Keeps the unmap counts of sequences for the production of a graph
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236 file_order.append(file) #Keeps the names of SAM files with the order of reading by the fuction (avoid problems due to multiprocesssing)
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237 samples.append(collapsed_mirnas) # return the processed detected miRNAs
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238 data.append([case,file,collapsed_mirnas,sorted_uni_arms])
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239 ini_sample.append(filter_sam) # returns the filtered sam file
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240
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241 l.release()
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242
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243
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244 ######################################################################################################################################
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245
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246
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247 """
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248
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249 Read a sam file from Bowtie and do the followings:
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250
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251 1) Remove reverse stranded mapped reads
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252 2) Remove unmapped reads
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253 3) Remove all sequences with reads less than 11 reads
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254 4) Sort the arms with the most sequences in decreading rate
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255 5) Sort the sequences of every arm with the most reads in decreasing rate
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256 6) Calculate total number of sequences of every arm
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257 7) Calculate total number of reads of sequences of every arm.
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258 8) Store all the informations in a txt file
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259
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260 """
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261
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262 def non_sam_edit(mature_mirnas,path,file,case,l,data,file_order,n_deseq,names_n_seqs):
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263
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264 # read the sam file
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265 ini_sam=read(path,0)
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266 main_sam = [x.rstrip("\n").split("\t") for x in ini_sam if "@" not in x.split("\t")[0]]
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267 unique_seq=[]
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268 unique_seq = [x for x in main_sam if x[1] == '4' and len(x[9])>=18 and len(x[9])<=26]
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269
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270 uni_seq=[]
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271
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272 # Calculate the shifted positions for every non template mirna and add them to the name of it
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273 sorted_uni_arms = []
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274 for i in range(1,len(mature_mirnas),2):
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275 tmp_count_reads = 0 # calculate the total number of reads
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276 tmp_count_seq = 0 # calculate the total number of sequences
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277
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278 for j in range(len(unique_seq)):
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279
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280 temp_mature = mature_mirnas[i].strip().replace("U", "T")
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281
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282 # Detection of differences between the canonical miRNA and the detected non template miRNA
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283 if temp_mature in unique_seq[j][9]:
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284
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285 off_part = longestSubstring(temp_mature, unique_seq[j][9])
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286
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287 mat_diff = temp_mature.split(off_part)
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288 mat_diff = [len(mat_diff[0]), len(mat_diff[1])]
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289
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290 unique_diff = unique_seq[j][9].split(off_part)
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291 if len(unique_diff)<=2:
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292 unique_diff = [len(unique_diff[0]), len(unique_diff[1])]
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293
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294 pre_pos = mat_diff[0]-unique_diff[0]
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295 post_pos = unique_diff[1]-mat_diff[1]
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296
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297 lengthofmir = len(off_part) + post_pos
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298 if pre_pos == 0 and post_pos<4:
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299 tmp_count_reads = tmp_count_reads + int(unique_seq[j][0].split("-")[1])
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300 tmp_count_seq = tmp_count_seq + 1
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301
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302 t_name=unique_seq[j].copy()
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303 t_name[2]=mature_mirnas[i - 1].split(" ")[0][1:] + "_nont_" + str(pre_pos) + "_" + '{:+d}'.format(post_pos) + "_" + str(unique_seq[j][9][len(off_part):])
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304 uni_seq.append(t_name)
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305 # metrics for the production of database
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306 if tmp_count_reads != 0 and tmp_count_seq != 0:
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307 sorted_uni_arms.append([mature_mirnas[i-1].split(" ")[0][1:], tmp_count_seq, tmp_count_reads])
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308
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309 sorted_uni_arms = sorted(sorted_uni_arms, key=lambda x: x[1], reverse=True)
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310 unique_seq = list(map(list, OrderedDict.fromkeys(map(tuple,uni_seq))))
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311
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312 # Output variables
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313 l.acquire()
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314 if case=="c" or case=="t":
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315 names_n_seqs.extend([[y[2],y[9]] for y in unique_seq if y[2]!="*"])
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316 n_deseq.append([[x[2], x[0].split('-')[1], x[9]] for x in unique_seq if x[2]!="*"])
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317 file_order.append(file)
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318 data.append([case,file,unique_seq,sorted_uni_arms])
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319 l.release()
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320
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321 #################################################################################################################################################################################################################
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322
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323 def black_white(mirna_names_1,mirna_names_2,group,manager):
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324
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325 add_names = [x for x in mirna_names_1 if x not in mirna_names_2]
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326 add_names.sort()
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327 add_names = list(add_names for add_names,_ in itertools.groupby(add_names))
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328
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329 group.sort()
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330 group = list(group for group,_ in itertools.groupby(group))
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331
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332 zeros=["0"]*(len(group[0])-2)
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333 [add_names[i].extend(zeros) for i,_ in enumerate(add_names)]
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334 group=group+add_names
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335
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336 manager.extend(group)
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337
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338 ################################################################################################################################################################################################################################
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339
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340 def merging_dupes(group,f_dupes):
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341
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342 dupes=[]
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343 final_mat =[]
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344
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345 for num,_ in enumerate(group):
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346
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347 if group[num][1] not in final_mat and group[num][0] not in final_mat:
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348 final_mat.append(group[num][1])
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349 final_mat.append(group[num][0])
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350 else:
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351 dupes.append(group[num][1])
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352
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353
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354 dupes=list(set(dupes))
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355
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356 dupes=[[x] for x in dupes]
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357
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358 for x in group:
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359 for y in dupes:
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360 if x[1]==y[0]:
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361 fl=0
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362 if len(y)==1:
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363 y.append(x[0])
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364 else:
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365 for i in range(1,len(y)):
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366 if y[i].split("_")[0]==x[0].split("_")[0]:
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367 fl=1
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368 if len(x[0])<len(y[i]):
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369 del y[i]
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370 y.append(x[0])
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371 break
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372
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373 if fl==0:
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374 y.append((x[0]))
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375
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376 for y in dupes:
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377 if len(y)>2:
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378 for i in range(len(y)-1,1,-1):
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379 y[1]=y[1]+"/"+y[i]
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380 del y[i]
|
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381
|
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382 f_dupes.extend(dupes)
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|
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383
|
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|
384 ##########################################################################################################################################################################################################################################
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385
|
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386 def apply_merging_dupes(group,dupes,managger):
|
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387
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388 for x in group:
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389 for y in dupes:
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390 if x[1]==y[0]:
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391 x[0]=y[1]
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392
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393 group.sort()
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|
394 group=list(group for group,_ in itertools.groupby(group))
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395 managger.extend(group)
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396
|
|
|
397 ###############################################################################################################################################################################################################################
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398
|
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399
|
|
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400 def filter_low_counts(c_group,t_group,fil_c_group,fil_t_group,per,counts):
|
|
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401
|
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|
402 t_group_new=[]
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403 c_group_new=[]
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404
|
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405 percent=int(per)/100
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406 c_col_filter=round(percent*(len(c_group[1])-2))
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|
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407 t_col_filter=round(percent*(len(t_group[1])-2))
|
|
|
408
|
|
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409 for i, _ in enumerate(c_group):
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|
410 c_cols=0
|
|
|
411 t_cols=0
|
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|
412
|
|
|
413 c_cols=sum([1 for j in range(len(c_group[i])-2) if int(c_group[i][j+2])>=int(counts)])
|
|
|
414 t_cols=sum([1 for j in range(len(t_group[i])-2) if int(t_group[i][j+2])>=int(counts)])
|
|
|
415
|
|
|
416 if c_cols>=c_col_filter or t_cols>=t_col_filter:
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|
417 t_group_new.append(t_group[i])
|
|
|
418 c_group_new.append(c_group[i])
|
|
|
419
|
|
|
420 fil_c_group.extend(c_group_new)
|
|
|
421 fil_t_group.extend(t_group_new)
|
|
|
422
|
|
|
423 ##################################################################################################################################################################################################################
|
|
|
424
|
|
|
425
|
|
|
426 def write_main(raw_con, raw_tre, fil_con, fil_tre, con_file_order, tre_file_order, flag, group_name1, group_name2, per):
|
|
|
427
|
|
|
428 if flag == 1 and int(per)!=-1:
|
|
|
429 fp = open('Counts/Filtered '+group_name2 +' Templated Counts', 'w')
|
|
|
430 fp.write("Name\t")
|
|
|
431 fp.write("Sequence")
|
|
|
432 for y in tre_file_order:
|
|
|
433 fp.write("\t"+y)
|
|
|
434
|
|
|
435 for x in fil_tre:
|
|
|
436 fp.write("\n%s" % "\t".join(x))
|
|
|
437 fp.close()
|
|
|
438
|
|
|
439 fp = open('Counts/Filtered '+group_name1+' Templated Counts', 'w')
|
|
|
440 fp.write("Name\t")
|
|
|
441 fp.write("Sequence")
|
|
|
442 for y in con_file_order:
|
|
|
443 fp.write("\t"+y)
|
|
|
444
|
|
|
445 for x in fil_con:
|
|
|
446 fp.write("\n%s" % "\t".join(x))
|
|
|
447 fp.close()
|
|
|
448
|
|
|
449
|
|
|
450 if flag == 2 and int(per)!=-1:
|
|
|
451 fp = open('Counts/Filtered '+group_name2+' Non-Templated Counts', 'w')
|
|
|
452 fp.write("Name\t")
|
|
|
453 fp.write("Sequence")
|
|
|
454 for y in tre_file_order:
|
|
|
455 fp.write("\t"+y)
|
|
|
456
|
|
|
457
|
|
|
458 for x in fil_tre:
|
|
|
459 fp.write("\n%s" % "\t".join(x))
|
|
|
460 fp.close()
|
|
|
461
|
|
|
462 fp = open('Counts/Filtered '+group_name1+' Non-Templated Counts', 'w')
|
|
|
463 fp.write("Name\t")
|
|
|
464 fp.write("Sequence")
|
|
|
465 for y in con_file_order:
|
|
|
466 fp.write("\t"+y)
|
|
|
467
|
|
|
468 for x in fil_con:
|
|
|
469 fp.write("\n%s" % "\t".join(x))
|
|
|
470 fp.close()
|
|
|
471
|
|
|
472
|
|
|
473 if flag == 1:
|
|
|
474 fp = open('Counts/Raw '+group_name2+' Templated Counts', 'w')
|
|
|
475 fp.write("Name\t")
|
|
|
476 fp.write("Sequence")
|
|
|
477 for y in tre_file_order:
|
|
|
478 fp.write("\t"+y)
|
|
|
479
|
|
|
480 for x in raw_tre:
|
|
|
481 fp.write("\n%s" % "\t".join(x))
|
|
|
482 fp.close()
|
|
|
483
|
|
|
484 fp = open('Counts/Raw '+group_name1+' Templated Counts', 'w')
|
|
|
485 fp.write("Name\t")
|
|
|
486 fp.write("Sequence")
|
|
|
487 for y in con_file_order:
|
|
|
488 fp.write("\t"+y)
|
|
|
489
|
|
|
490 for x in raw_con:
|
|
|
491 fp.write("\n%s" % "\t".join(x))
|
|
|
492 fp.close()
|
|
|
493
|
|
|
494
|
|
|
495 if flag == 2:
|
|
|
496 fp = open('Counts/Raw '+group_name2+' Non-Templated Counts', 'w')
|
|
|
497 fp.write("Name\t")
|
|
|
498 fp.write("Sequence")
|
|
|
499 for y in tre_file_order:
|
|
|
500 fp.write("\t"+y)
|
|
|
501
|
|
|
502
|
|
|
503 for x in raw_tre:
|
|
|
504 fp.write("\n%s" % "\t".join(x))
|
|
|
505 fp.close()
|
|
|
506
|
|
|
507 fp = open('Counts/Raw '+group_name1+' Non-Templated Counts', 'w')
|
|
|
508 fp.write("Name\t")
|
|
|
509 fp.write("Sequence")
|
|
|
510 for y in con_file_order:
|
|
|
511 fp.write("\t"+y)
|
|
|
512
|
|
|
513 for x in raw_con:
|
|
|
514 fp.write("\n%s" % "\t".join(x))
|
|
|
515 fp.close()
|
|
|
516
|
|
|
517
|
|
|
518 #########################################################################################################################################
|
|
|
519
|
|
|
520 def temp_counts_to_diff(names,samp,folder):
|
|
|
521
|
|
|
522 for i in range(2,len(samp[0])):
|
|
|
523
|
|
|
524 fp = open(folder+names[i-2]+'.txt','w')
|
|
|
525 fp.write("miRNA id"+"\t"+names[i-2]+"\n")
|
|
|
526
|
|
|
527 for x in samp:
|
|
|
528 fp.write("%s" % "\t".join([x[0],x[i]])+"\n")
|
|
|
529 fp.close()
|
|
|
530
|
|
|
531 ##################################################################################################################
|
|
|
532
|
|
|
533 def DB_write(con,name,unique_seq,sorted_uni_arms,f):
|
|
|
534
|
|
|
535 if f==1:
|
|
|
536 # Write a txt file with all the information
|
|
|
537 if con=="c":
|
|
|
538 fp = open('split1/'+name, 'w')
|
|
|
539
|
|
|
540 fp.write("%s\t%-42s\t%s\n\n" % ("Number of Reads","Name of isomir","Sequence"))
|
|
|
541 if con=="t":
|
|
|
542 fp = open('split2/'+name, 'w')
|
|
|
543 fp.write("%s\t%-42s\t%s\n\n" % ("Number of Reads","Name of isomir","Sequence"))
|
|
|
544
|
|
|
545
|
|
|
546 for i in range(len(sorted_uni_arms)):
|
|
|
547 temp = []
|
|
|
548 for j in range(len(unique_seq)):
|
|
|
549
|
|
|
550 if sorted_uni_arms[i][0] in unique_seq[j][2].split("_")[0]:
|
|
|
551
|
|
|
552 temp.append(unique_seq[j])
|
|
|
553
|
|
|
554 temp = sorted(temp, key=lambda x: int(x[0].split('-')[1]), reverse=True)
|
|
|
555 fp.write("*********************************************************************************************************\n")
|
|
|
556 fp.write("%-8s\t%-22s\t%-25s\t%-30s\t%s\n" % ("|",str(sorted_uni_arms[i][0]),"Sequence count = "+str(sorted_uni_arms[i][1]),"Total reads = "+str(sorted_uni_arms[i][2]),"|"))
|
|
|
557 fp.write("*********************************************************************************************************\n\n")
|
|
|
558 [fp.write("%-8s\t%-40s\t%s\n" % (x[0].split("-")[1], x[2],x[9])) for x in temp]
|
|
|
559 fp.write("\n" + "\n")
|
|
|
560 fp.close()
|
|
|
561
|
|
|
562 if f==2:
|
|
|
563
|
|
|
564 if con=="c":
|
|
|
565 fp = open('split3/'+name, 'w')
|
|
|
566 fp.write("%s\t%-42s\t%s\n\n" % ("Number of Reads","Name of isomir","Sequence"))
|
|
|
567 if con=="t":
|
|
|
568 fp = open('split4/'+name, 'w')
|
|
|
569 fp.write("%s\t%-42s\t%s\n\n" % ("Number of Reads","Name of isomir","Sequence"))
|
|
|
570
|
|
|
571
|
|
|
572 for i in range(len(sorted_uni_arms)):
|
|
|
573 temp = []
|
|
|
574 for j in range(len(unique_seq)):
|
|
|
575 if sorted_uni_arms[i][0]==unique_seq[j][2].split("_nont_")[0]:
|
|
|
576 temp.append(unique_seq[j])
|
|
|
577 if temp!=[]:
|
|
|
578 temp = sorted(temp, key=lambda x: int(x[0].split('-')[1]), reverse=True)
|
|
|
579 fp.write("*********************************************************************************************************\n")
|
|
|
580 fp.write("%-8s\t%-22s\t%-25s\t%-30s\t%s\n" % ("|",str(sorted_uni_arms[i][0]),"Sequence count = "+str(sorted_uni_arms[i][1]),"Total reads = "+str(sorted_uni_arms[i][2]),"|"))
|
|
|
581 fp.write("*********************************************************************************************************\n\n")
|
|
|
582 [fp.write("%-8s\t%-40s\t%s\n" % (x[0].split("-")[1], x[2],x[9])) for x in temp]
|
|
|
583 fp.write("\n" + "\n")
|
|
|
584 fp.close()
|
|
|
585
|
|
|
586
|
|
|
587 ##########################################################################################################################
|
|
|
588
|
|
|
589 def new_mat_seq(pre_unique_seq,mat_mirnas,l):
|
|
|
590
|
|
|
591 unique_iso = []
|
|
|
592 for x in pre_unique_seq:
|
|
|
593 if len(x[2].split("_"))==3:
|
|
|
594 for y in pre_unique_seq:
|
|
|
595 if x[2] in y[2] and int(x[0].split("-")[1])<int(y[0].split("-")[1]):
|
|
|
596 if any(y[2] in lst2 for lst2 in unique_iso)==False:
|
|
|
597 y[2]=">"+y[2]
|
|
|
598 unique_iso.append(y)
|
|
|
599 l.acquire()
|
|
|
600 for x in unique_iso:
|
|
|
601 mat_mirnas.append(x[2])
|
|
|
602 mat_mirnas.append(x[9])
|
|
|
603 l.release()
|
|
|
604
|
|
|
605 #########################################################################################################################
|
|
|
606
|
|
|
607 def merging_names(ini_mat,new):
|
|
|
608
|
|
|
609 dupes=[]
|
|
|
610 final_mat =[]
|
|
|
611
|
|
|
612 for num in range(len(ini_mat)):
|
|
|
613
|
|
|
614 if ini_mat[num][1] not in final_mat and ini_mat[num][0] not in final_mat:
|
|
|
615 final_mat.append(ini_mat[num][1])
|
|
|
616 final_mat.append(ini_mat[num][0])
|
|
|
617 else:
|
|
|
618 dupes.append(ini_mat[num][1])
|
|
|
619
|
|
|
620 dupes=list(set(dupes))
|
|
|
621
|
|
|
622 for i in range(len(dupes)):
|
|
|
623 dupes[i]=[dupes[i]]
|
|
|
624
|
|
|
625 for x in ini_mat:
|
|
|
626 for y in dupes:
|
|
|
627 if x[1]==y[0]:
|
|
|
628 fl=0
|
|
|
629 if len(y)==1:
|
|
|
630 y.append(x[0])
|
|
|
631 else:
|
|
|
632 for i in range(1,len(y)):
|
|
|
633 if y[i].split("_")[0]==x[0].split("_")[0]:
|
|
|
634 fl=1
|
|
|
635 if len(x[0])<len(y[i]):
|
|
|
636 del y[i]
|
|
|
637 y.append(x[0])
|
|
|
638 break
|
|
|
639
|
|
|
640 if fl==0:
|
|
|
641 y.append((x[0]))
|
|
|
642
|
|
|
643 for y in dupes:
|
|
|
644 if len(y)>2:
|
|
|
645 for i in range(len(y)-1,1,-1):
|
|
|
646 y[1]=y[1]+"/"+y[i]
|
|
|
647 del y[i]
|
|
|
648
|
|
|
649
|
|
|
650 for x in ini_mat:
|
|
|
651 for y in dupes:
|
|
|
652 if x[1]==y[0]:
|
|
|
653 x[0]=y[1]
|
|
|
654
|
|
|
655 ini_mat.sort()
|
|
|
656 ini_mat=list(ini_mat for ini_mat,_ in itertools.groupby(ini_mat))
|
|
|
657
|
|
|
658 new.extend(ini_mat)
|
|
|
659
|
|
|
660
|
|
|
661 ######################################################################################################################################################
|
|
|
662
|
|
|
663 def nontemp_counts_to_diff(tem_names,tem_samp,non_names,non_samp,folder):
|
|
|
664
|
|
|
665 for i in range(2,len(tem_samp[0])):
|
|
|
666
|
|
|
667 fp = open(folder+tem_names[i-2]+'.txt','w')
|
|
|
668 fp.write("miRNA id"+"\t"+tem_names[i-2]+"\n")
|
|
|
669
|
|
|
670 for x in tem_samp:
|
|
|
671 fp.write("%s" % "\t".join([x[0],x[i]])+"\n")
|
|
|
672
|
|
|
673 for j in range(len(non_names)):
|
|
|
674 if non_names[j]==tem_names[i-2]:
|
|
|
675 for x in non_samp:
|
|
|
676 fp.write("%s" % "\t".join([x[0],x[j+2]])+"\n")
|
|
|
677 fp.close()
|
|
|
678
|
|
|
679 ###################################################################################################################################################################################################################
|
|
|
680
|
|
|
681 """
|
|
|
682
|
|
|
683 This function downloads all the miRNAs of all the species from MirBase
|
|
|
684 and filters them by the requested organism
|
|
|
685
|
|
|
686 input : Organism
|
|
|
687 output: A list with the miRNA sequences in fasta format
|
|
|
688
|
|
|
689 """
|
|
|
690
|
|
|
691 def download_matures(matures,org_name):
|
|
|
692
|
|
|
693 url = 'ftp://mirbase.org/pub/mirbase/CURRENT/mature.fa.gz'
|
|
|
694 data = urllib.request.urlopen(url).read()
|
|
|
695 file_mirna = gzip.decompress(data).decode('utf-8')
|
|
|
696 file_mirna = file_mirna.split("\n")
|
|
|
697
|
|
|
698 for i in range(0,len(file_mirna)-1,2):
|
|
|
699
|
|
|
700 if org_name in file_mirna[i]:
|
|
|
701 matures.append(file_mirna[i])
|
|
|
702 matures.append(file_mirna[i+1])
|
|
|
703
|
|
|
704 ###################################################################################################################################################################################################################
|
|
|
705
|
|
|
706
|
|
|
707 """
|
|
|
708
|
|
|
709 This function keeps all mirna isoforms which are detected on SAM files from the first part of the analysis
|
|
|
710 These isoforms will be used as refence sequences with canonical (ref) mirnas for the detection of non-template
|
|
|
711 mirnas
|
|
|
712
|
|
|
713 """
|
|
|
714
|
|
|
715
|
|
|
716 def non_template_ref(c_samples,t_samples,all_isoforms):
|
|
|
717
|
|
|
718 pre_uni_seq_con = list(c_samples)
|
|
|
719 pre_uni_seq_tre = list(t_samples)
|
|
|
720
|
|
|
721 for x in pre_uni_seq_con:
|
|
|
722 for y in x:
|
|
|
723 #if ">"+y[2] not in all_isoforms and ")_" in y[2] :
|
|
|
724 if ">"+y[2] not in all_isoforms and "_t_" in y[2] :
|
|
|
725 all_isoforms.append(">"+y[2])
|
|
|
726 all_isoforms.append(y[9])
|
|
|
727
|
|
|
728 for x in pre_uni_seq_tre:
|
|
|
729 for y in x:
|
|
|
730 #if ">"+y[2] not in all_isoforms and ")_" in y[2]:
|
|
|
731 if ">"+y[2] not in all_isoforms and "_t_" in y[2] :
|
|
|
732 all_isoforms.append(">"+y[2])
|
|
|
733 all_isoforms.append(y[9])
|
|
|
734
|
|
|
735 ################################################################################################################################################################################################
|
|
|
736
|
|
|
737 """
|
|
|
738
|
|
|
739 This function adds the uncommon detected miRNAs among samples.
|
|
|
740 As a result all samples will have the same length.
|
|
|
741
|
|
|
742 """
|
|
|
743
|
|
|
744 def uncommon_mirnas(sample,mir_names,l,new_d,sample_name,sample_order):
|
|
|
745
|
|
|
746 for y in mir_names:
|
|
|
747 flag=0
|
|
|
748 for x in sample:
|
|
|
749 if y[0]==x[0]: # check if miRNA exists in the sample
|
|
|
750 flag=1
|
|
|
751 break
|
|
|
752 if flag==0:
|
|
|
753 sample.append([y[0],"0",y[1]]) # add the name of mirna to the sample with zero counts and its sequence
|
|
|
754
|
|
|
755 # sorting and remove duplicates
|
|
|
756 sample.sort(key=lambda x: x[0])
|
|
|
757 sample=list(sample for sample,_ in itertools.groupby(sample))
|
|
|
758
|
|
|
759 # Return the updated sample
|
|
|
760 l.acquire()
|
|
|
761 new_d.append(sample)
|
|
|
762 sample_order.append(sample_name)
|
|
|
763 l.release()
|
|
|
764
|
|
|
765 ###############################################################################################################################################################################################
|
|
|
766
|
