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1 import itertools
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2 import time
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3 import sys
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4 import os
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5 import urllib.request
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6 import gzip
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7 from multiprocessing import Process, Queue, Lock, Pool, Manager, Value
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8 import subprocess
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9 import argparse
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10 from collections import OrderedDict
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11 from matplotlib.backends.backend_pdf import PdfPages
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12 import pandas as pd
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13 from math import pi
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14 import numpy as np
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15 import matplotlib.pyplot as plt
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16 from matplotlib.ticker import PercentFormatter
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17 import seaborn as sns
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18 import scipy.stats as stats
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19 from plotnine import *
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20 import math
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21 import re
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22 import matplotlib.ticker as mtick
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23 import copy
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24
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25
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26
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27
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28 """---------------------- Simple Functions -----------------------"""
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29
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30 # Read a file and return it as a list
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31 def read(path, flag):
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32 if flag == 0:
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33 with open(path) as fp:
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34 file=fp.readlines()
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35 fp.close()
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36 return file
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37
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38 if flag == 1:
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39 with open(path) as fp:
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40 file = fp.read().splitlines()
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41 fp.close()
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42 return file
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43
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44 # Write a list to a txt file
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45 def write(path, list):
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46 with open(path,'w') as fp:
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47 for x in list:
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48 fp.write(str("\t".join(x[1:-1])))
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49 fp.close()
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50
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51 """---------------------- RNA-seq Functions ----------------------"""
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52
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53 # Detect the longest common substring sequence between two mirnas
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54 def longestSubstring(str1, str2):
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55
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56 from difflib import SequenceMatcher
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57 # initialize SequenceMatcher object with
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58 # input string
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59 seqMatch = SequenceMatcher(None, str1, str2)
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60
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61 # find match of longest sub-string
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62 # output will be like Match(a=0, b=0, size=5)
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63 match = seqMatch.find_longest_match(0, len(str1), 0, len(str2))
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64
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65 # print longest substring
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66 if (match.size != 0):
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67 return str1[match.a: match.a + match.size]
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68 else:
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69 print('No longest common sub-string found')
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70
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71
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72
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73 ########################################################################################################################################################
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74 def collapse_sam(path):
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75
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76 ini_sam=read(path,0)
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77 main_sam = [x.rstrip("\n").split("\t") for x in ini_sam if "@" not in x.split("\t")[0]]
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78 intro_sam = [x.rstrip("\n").split("\t") for x in ini_sam if "@" in x.split("\t")[0]]
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79
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80 uni_seq = []
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81 for x in main_sam:
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82
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83 if [x[2], x[9]] not in uni_seq:
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84 uni_seq.append([x[2], x[9]])
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85
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86 new_main_sam=[]
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87 incr_num=0
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88 for i in range(len(uni_seq)):
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89 count=0
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90 incr_num+=1
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91 for y in main_sam:
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92 if uni_seq[i][1]==y[9] and uni_seq[i][0]==y[2]:
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93 count+=1
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94 temp=y
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95 temp[10]="~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
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96 temp[0]=str(incr_num)+"-"+str(count)
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97 new_main_sam.append(temp)
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98
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99 new_sam=intro_sam+new_main_sam
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100
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101 return new_sam
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102
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103 #################################################################################################################################################################
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104
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105 def sam(mature_mirnas,path,name,con,l,samples,data,names,unmap_seq,samples_mirna_names,deseq,LHE_names,umi,ini_sample,unmap_counts):
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106
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107 # read the sam file
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108
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109 ini_sam=read(path,0)
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110 new_main_sam = [x.rstrip("\n").split("\t") for x in ini_sam if "@" not in x.split("\t")[0]]
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111 unique_seq = [x for x in new_main_sam if x[1] == '0' and len(x[9])>=18 and len(x[9])<=26]
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112
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113 # Calculate the shifted positions for every isomir and add them to the name of it
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114 sorted_uni_arms = []
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115
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116 for i in range(len(mature_mirnas)):
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117 tmp_count_reads = 0 # calculate the total number of reads
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118 tmp_count_seq = 0 # calculate the total number of sequences
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119 for j in range(len(unique_seq)):
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120
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121 if mature_mirnas[i] == unique_seq[j][2]:
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122
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123 temp_mature = mature_mirnas[i+1]
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124 off_part = longestSubstring(temp_mature, unique_seq[j][9])
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125
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126 mat_diff = temp_mature.split(off_part)
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127 mat_diff = [len(mat_diff[0]), len(mat_diff[1])]
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128
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129 unique_diff = unique_seq[j][9].split(off_part)
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130 unique_diff = [len(unique_diff[0]), len(unique_diff[1])]
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131
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132 # Problem with hsa-miR-8485
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133 if mat_diff[1]!=0 and unique_diff[1]!=0:
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134 unique_seq[j]=1
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135 pre_pos = 0
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136 post_pos = 0
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137
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138 elif mat_diff[0]!=0 and unique_diff[0]!=0:
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139 unique_seq[j]=1
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140 pre_pos = 0
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141 post_pos = 0
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142
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143 else:
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144 pre_pos = mat_diff[0]-unique_diff[0]
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145 post_pos = unique_diff[1]-mat_diff[1]
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146 tmp_count_reads = tmp_count_reads + int(unique_seq[j][0].split("-")[1])
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147 tmp_count_seq = tmp_count_seq+1
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148
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149
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150 if pre_pos != 0 or post_pos != 0:
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151 if pre_pos == 0:
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152 unique_seq[j][2] = unique_seq[j][2] + "_" +str(pre_pos) + "_" + '{:+d}'.format(post_pos)
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153 elif post_pos == 0:
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154 unique_seq[j][2] = unique_seq[j][2] + "_" + '{:+d}'.format(pre_pos) + "_" + str(post_pos)
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155 else:
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156 unique_seq[j][2] = unique_seq[j][2]+"_"+'{:+d}'.format(pre_pos)+"_"+'{:+d}'.format(post_pos)
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157
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158 for x in range(unique_seq.count(1)):
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159 unique_seq.remove(1)
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160 if tmp_count_reads != 0 and tmp_count_seq != 0:
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161 sorted_uni_arms.append([mature_mirnas[i], tmp_count_seq, tmp_count_reads])
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162
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163 # Store name of arms, number of sequences and number of reads
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164 sorted_uni_arms = sorted(sorted_uni_arms, key=lambda x: x[1], reverse=True)
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165
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166 for y in sorted_uni_arms:
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167 counts=0
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168 seqs=0
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169 for x in unique_seq:
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170 if y[0]==x[2].split("_")[0]+"_"+x[2].split("_")[1]:
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171 counts+=int(x[0].split("-")[1])
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172 seqs+=1
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173
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174 y[1]=seqs
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175 y[2]=counts
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176
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177 LHE=[]
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178
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179 l.acquire()
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180 if con=="c":
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181 LHE.extend(z[2] for z in unique_seq)
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182 for y in unique_seq:
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183 samples_mirna_names.append([y[2],y[9]])
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184 deseq.append([[x[2], x[0].split('-')[1], x[9]] for x in unique_seq])
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185 LHE_names.extend(LHE)
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186 unmap_seq.value += sum([1 for x in new_main_sam if x[1] == '4'])
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187 unmap_counts.value += sum([int(x[0].split("-")[1]) for x in new_main_sam if x[1] == '4'])
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188 names.append(name)
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189 samples.append(unique_seq)
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190 data.append([con,name,unique_seq,sorted_uni_arms])
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191 ini_sample.append(new_main_sam)
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192
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193 if con=="t":
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194 LHE.extend(z[2] for z in unique_seq)
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195 for y in unique_seq:
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196 samples_mirna_names.append([y[2],y[9]])
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197 deseq.append([[x[2], x[0].split('-')[1], x[9]] for x in unique_seq])
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198 LHE_names.extend(LHE)
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199 unmap_seq.value += sum([1 for x in new_main_sam if x[1] == '4'])
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200 unmap_counts.value += sum([int(x[0].split("-")[1]) for x in new_main_sam if x[1] == '4'])
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201 names.append(name)
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202 samples.append(unique_seq)
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203 data.append([con,name,unique_seq,sorted_uni_arms])
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204 ini_sample.append(new_main_sam)
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205 l.release()
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206
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207
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208 ######################################################################################################################################
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209 """
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210 Read a sam file from Bowtie and do the followings:
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211
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212 1) Remove reverse stranded mapped reads
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213 2) Remove unmapped reads
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214 3) Remove all sequences with reads less than 11 reads
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215 4) Sort the arms with the most sequences in decreading rate
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216 5) Sort the sequences of every arm with the most reads in decreasing rate
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217 6) Calculate total number of sequences of every arm
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218 7) Calculate total number of reads of sequences of every arm.
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219 8) Store all the informations in a txt file
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220
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221 """
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222
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223 def non_sam(mature_mirnas,path,name,con,l,data,names,n_deseq,n_samples_mirna_names,n_LHE_names):
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224
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225
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226 ini_sam=read(path,0)
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227 new_main_sam = [x.rstrip("\n").split("\t") for x in ini_sam if "@" not in x.split("\t")[0]]
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228 unique_seq=[]
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229 unique_seq = [x for x in new_main_sam if x[1] == '4' and len(x[9])>=18 and len(x[9])<=26]
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230 uni_seq=[]
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231
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232 # Calculate the shifted positions for every isomir and add them to the name of it
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233 sorted_uni_arms = []
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234 for i in range(1,len(mature_mirnas),2):
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235 tmp_count_reads = 0 # calculate the total number of reads
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236 tmp_count_seq = 0 # calculate the total number of sequences
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237
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238 for j in range(len(unique_seq)):
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239
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240 temp_mature = mature_mirnas[i].strip().replace("U", "T")
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241
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242 if temp_mature in unique_seq[j][9]:
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243
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244 off_part = longestSubstring(temp_mature, unique_seq[j][9])
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245
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246 mat_diff = temp_mature.split(off_part)
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247 mat_diff = [len(mat_diff[0]), len(mat_diff[1])]
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248
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249 unique_diff = unique_seq[j][9].split(off_part)
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250 if len(unique_diff)<=2:
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251 unique_diff = [len(unique_diff[0]), len(unique_diff[1])]
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252
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253 pre_pos = mat_diff[0]-unique_diff[0]
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254 post_pos = unique_diff[1]-mat_diff[1]
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255
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256 lengthofmir = len(off_part) + post_pos
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257 if pre_pos == 0:
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258 tmp_count_reads = tmp_count_reads + int(unique_seq[j][0].split("-")[1])
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259 tmp_count_seq = tmp_count_seq + 1
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260
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261 if pre_pos == 0:
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262 t_name=copy.deepcopy(unique_seq[j])
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263 t_name[2]=mature_mirnas[i - 1] + "__" + str(pre_pos) + "_" + '{:+d}'.format(post_pos) + "_" + str(unique_seq[j][9][len(off_part):])
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264 uni_seq.append(t_name)
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265
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266 if tmp_count_reads != 0 and tmp_count_seq != 0:
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267 sorted_uni_arms.append([mature_mirnas[i-1], tmp_count_seq, tmp_count_reads])
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268
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269
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270 sorted_uni_arms = sorted(sorted_uni_arms, key=lambda x: x[1], reverse=True)
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271 unique_seq = list(map(list, OrderedDict.fromkeys(map(tuple,uni_seq))))
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272
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273 LHE=[]
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274
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275 l.acquire()
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276 if con=="c":
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277 LHE.extend(x[2] for x in unique_seq if x[2]!="*")
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278 for x in unique_seq:
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279 if x[2]!="*":
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280 n_samples_mirna_names.append([x[2],x[9]])
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281 n_deseq.append([[x[2], x[0].split('-')[1], x[9]] for x in unique_seq if x[2]!="*"])
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282 n_LHE_names.extend(LHE)
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283 names.append(name)
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284 data.append([con,name,unique_seq,sorted_uni_arms])
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285
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286
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287 if con=="t":
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288 LHE.extend(x[2] for x in unique_seq if x[2]!="*")
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289 for x in unique_seq:
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290 if x[2]!="*":
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291 n_samples_mirna_names.append([x[2],x[9]])
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292 n_deseq.append([[x[2], x[0].split('-')[1], x[9]] for x in unique_seq if x[2]!="*"])
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293 n_LHE_names.extend(LHE)
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294 names.append(name)
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295 data.append([con,name,unique_seq,sorted_uni_arms])
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296 l.release()
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297
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298 #################################################################################################################################################################################################################
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299
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300 def deseq2_temp(samples_mirna_names,deseq,con,l):
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301
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302 samples_mirna_names.sort(key=lambda x:[0])
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303
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304 for i in range(len(deseq)):
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305 for y in samples_mirna_names:
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306 flag = 0
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307 for x in deseq[i]:
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308 if y[0] == x[0]:
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309 flag = 1
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310 break
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311
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312 if flag == 0:
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313 deseq[i].append([y[0], "0", y[1]])
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314
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315 [deseq[i].sort(key=lambda x: x[0]) for i, _ in enumerate(deseq)]
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316 deseq_final = [[x[0],x[2]] for x in deseq[0]]
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317 [deseq_final[z].append(deseq[i][j][1]) for z,_ in enumerate(deseq_final) for i, _ in enumerate(deseq) for j,_ in enumerate(deseq[i]) if deseq_final[z][0] == deseq[i][j][0]]
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318
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319 l.acquire()
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320 if con=="c":
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321 q1.put(deseq_final)
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322
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323 if con=="t":
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324 q2.put(deseq_final)
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325 l.release()
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326
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327
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328 ##################################################################################################################################################################################################################
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329
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330 def main_temp(LH2E, LH2E_names, LH8E, LH8E_names,flag,names_con,names_tre,filter_LH8E,filter_LH2E,raw_LH8E,raw_LH2E,per,count):
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331
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332 LH8E_add_names = [x for x in LH2E_names if x not in LH8E_names]
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333 LH2E_add_names = [x for x in LH8E_names if x not in LH2E_names]
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334
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335 LH8E_add_names.sort()
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336 LH2E_add_names.sort()
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337 LH8E_add_names = list(LH8E_add_names for LH8E_add_names,_ in itertools.groupby(LH8E_add_names))
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338 LH2E_add_names = list(LH2E_add_names for LH2E_add_names,_ in itertools.groupby(LH2E_add_names))
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339
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340 LH2E.sort()
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341 LH8E.sort()
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342 LH2E = list(LH2E for LH2E,_ in itertools.groupby(LH2E))
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343 LH8E = list(LH8E for LH8E,_ in itertools.groupby(LH8E))
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344
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345 zeros=["0"]*(len(LH8E[0])-2)
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346 [LH8E_add_names[i].extend(zeros) for i,_ in enumerate(LH8E_add_names)]
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347 LH8E=LH8E+LH8E_add_names
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348
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349 zeros=["0"]*(len(LH2E[0])-2)
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350 [LH2E_add_names[i].extend(zeros) for i,_ in enumerate(LH2E_add_names)]
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351 LH2E=LH2E+LH2E_add_names
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352
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353 dupes=[]
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354 final_LH2E =[]
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355
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356 for num,_ in enumerate(LH2E):
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357
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358 if LH2E[num][1] not in final_LH2E and LH2E[num][0] not in final_LH2E:
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359 final_LH2E.append(LH2E[num][1])
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360 final_LH2E.append(LH2E[num][0])
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361 else:
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362 dupes.append(LH2E[num][1])
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363
|
|
|
364 dupes=list(set(dupes))
|
|
|
365
|
|
|
366 dupes=[[x] for x in dupes]
|
|
|
367
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368 for x in LH2E:
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369 for y in dupes:
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370 if x[1]==y[0]:
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|
371 fl=0
|
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|
372 if len(y)==1:
|
|
|
373 y.append(x[0])
|
|
|
374 else:
|
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|
375 for i in range(1,len(y)):
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|
376 if y[i].split("_")[0]+"_"+y[i].split("_")[1]==x[0].split("_")[0]+"_"+x[0].split("_")[1]:
|
|
|
377 fl=1
|
|
|
378 if len(x[0])<len(y[i]):
|
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|
379 del y[i]
|
|
|
380 y.append(x[0])
|
|
|
381 break
|
|
|
382
|
|
|
383 if fl==0:
|
|
|
384 y.append((x[0]))
|
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385
|
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386 for y in dupes:
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387 if len(y)>2:
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388 for i in range(len(y)-1,1,-1):
|
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|
389 y[1]=y[1]+"/"+y[i]
|
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|
390 del y[i]
|
|
|
391
|
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392
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393 for x in LH2E:
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|
394 for y in dupes:
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|
395 if x[1]==y[0]:
|
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|
396 x[0]=y[1]
|
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|
397
|
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|
398 for x in LH8E:
|
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|
399 for y in dupes:
|
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|
400 if x[1]==y[0]:
|
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|
401 x[0]=y[1]
|
|
|
402
|
|
|
403
|
|
|
404
|
|
|
405 LH2E.sort()
|
|
|
406 LH2E=list(LH2E for LH2E,_ in itertools.groupby(LH2E))
|
|
|
407
|
|
|
408 LH8E.sort()
|
|
|
409 LH8E=list(LH8E for LH8E,_ in itertools.groupby(LH8E))
|
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410
|
|
|
411 if int(per)!=-1:
|
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|
412 percent=int(per)/100
|
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|
413
|
|
|
414 c_col_filter=round(percent*(len(LH2E[1])-2))
|
|
|
415 t_col_filter=round(percent*(len(LH8E[1])-2))
|
|
|
416
|
|
|
417 for i, _ in enumerate(LH2E):
|
|
|
418 c_cols=0
|
|
|
419 t_cols=0
|
|
|
420
|
|
|
421 c_cols=sum([1 for j in range(len(LH2E[i])-2) if int(LH2E[i][j+2])>=int(count)])
|
|
|
422 t_cols=sum([1 for j in range(len(LH8E[i])-2) if int(LH8E[i][j+2])>=int(count)])
|
|
|
423
|
|
|
424 if c_cols>=c_col_filter or t_cols>=t_col_filter:
|
|
|
425 filter_LH8E.append(LH8E[i])
|
|
|
426 filter_LH2E.append(LH2E[i])
|
|
|
427
|
|
|
428 raw_LH2E.extend(LH2E)
|
|
|
429 raw_LH8E.extend(LH8E)
|
|
|
430
|
|
|
431 ##################################################################################################################################################################################################################
|
|
|
432
|
|
|
433 def write_main(raw_LH2E, raw_LH8E, fil_LH2E, fil_LH8E, names_con, names_tre, flag, per, n1, n2):
|
|
|
434
|
|
|
435 if flag == 1 and int(per)!=-1:
|
|
|
436 fp = open('Counts/Filtered '+n2 +' Templated Counts', 'w')
|
|
|
437 fp.write("Name\t")
|
|
|
438 fp.write("Sequence")
|
|
|
439 for y in names_tre:
|
|
|
440 fp.write("\t"+y)
|
|
|
441
|
|
|
442 for x in fil_LH8E:
|
|
|
443 fp.write("\n%s" % "\t".join(x))
|
|
|
444 fp.close()
|
|
|
445
|
|
|
446 fp = open('Counts/Filtered '+n1+' Templated Counts', 'w')
|
|
|
447 fp.write("Name\t")
|
|
|
448 fp.write("Sequence")
|
|
|
449 for y in names_con:
|
|
|
450 fp.write("\t"+y)
|
|
|
451
|
|
|
452 for x in fil_LH2E:
|
|
|
453 fp.write("\n%s" % "\t".join(x))
|
|
|
454 fp.close()
|
|
|
455
|
|
|
456
|
|
|
457 if flag == 2 and int(per)!=-1:
|
|
|
458 fp = open('Counts/Filtered '+n2+' Non-Templated Counts', 'w')
|
|
|
459 fp.write("Name\t")
|
|
|
460 fp.write("Sequence")
|
|
|
461 for y in names_tre:
|
|
|
462 fp.write("\t"+y)
|
|
|
463
|
|
|
464
|
|
|
465 for x in fil_LH8E:
|
|
|
466 fp.write("\n%s" % "\t".join(x))
|
|
|
467 fp.close()
|
|
|
468
|
|
|
469 fp = open('Counts/Filtered '+n1+' Non-Templated Counts', 'w')
|
|
|
470 fp.write("Name\t")
|
|
|
471 fp.write("Sequence")
|
|
|
472 for y in names_con:
|
|
|
473 fp.write("\t"+y)
|
|
|
474
|
|
|
475 for x in fil_LH2E:
|
|
|
476 fp.write("\n%s" % "\t".join(x))
|
|
|
477 fp.close()
|
|
|
478
|
|
|
479
|
|
|
480 if flag == 1:
|
|
|
481 fp = open('Counts/Raw '+n2+' Templated Counts', 'w')
|
|
|
482 fp.write("Name\t")
|
|
|
483 fp.write("Sequence")
|
|
|
484 for y in names_tre:
|
|
|
485 fp.write("\t"+y)
|
|
|
486
|
|
|
487 for x in raw_LH8E:
|
|
|
488 fp.write("\n%s" % "\t".join(x))
|
|
|
489 fp.close()
|
|
|
490
|
|
|
491 fp = open('Counts/Raw '+n1+' Templated Counts', 'w')
|
|
|
492 fp.write("Name\t")
|
|
|
493 fp.write("Sequence")
|
|
|
494 for y in names_con:
|
|
|
495 fp.write("\t"+y)
|
|
|
496
|
|
|
497 for x in raw_LH2E:
|
|
|
498 fp.write("\n%s" % "\t".join(x))
|
|
|
499 fp.close()
|
|
|
500
|
|
|
501 if flag == 2:
|
|
|
502 fp = open('Counts/Raw '+n2+' Non-Templated Counts', 'w')
|
|
|
503 fp.write("Name\t")
|
|
|
504 fp.write("Sequence")
|
|
|
505 for y in names_tre:
|
|
|
506 fp.write("\t"+y)
|
|
|
507
|
|
|
508
|
|
|
509 for x in raw_LH8E:
|
|
|
510 fp.write("\n%s" % "\t".join(x))
|
|
|
511 fp.close()
|
|
|
512
|
|
|
513 fp = open('Counts/Raw '+n1+' Non-Templated Counts', 'w')
|
|
|
514 fp.write("Name\t")
|
|
|
515 fp.write("Sequence")
|
|
|
516 for y in names_con:
|
|
|
517 fp.write("\t"+y)
|
|
|
518
|
|
|
519 for x in raw_LH2E:
|
|
|
520 fp.write("\n%s" % "\t".join(x))
|
|
|
521 fp.close()
|
|
|
522
|
|
|
523 ####################################################################################################################################################################################################################
|
|
|
524
|
|
|
525 def ssamples(names,samp,folder,pro):
|
|
|
526
|
|
|
527 for i in range(2,len(samp[0])):
|
|
|
528
|
|
|
529 fp = open(folder+names[i-2]+'.txt','w')
|
|
|
530 fp.write("miRNA id"+"\t"+names[i-2]+"\n")
|
|
|
531
|
|
|
532 for x in samp:
|
|
|
533 fp.write("%s" % "\t".join([x[0],x[i]])+"\n")
|
|
|
534 fp.close()
|
|
|
535
|
|
|
536 ####################################################################################################################################################################################################################
|
|
|
537
|
|
|
538 def DB_write(con,name,unique_seq,sorted_uni_arms,f):
|
|
|
539
|
|
|
540 if f==1:
|
|
|
541 # Write a txt file with all the information
|
|
|
542 if con=="c":
|
|
|
543 fp = open('split1/'+name, 'w')
|
|
|
544
|
|
|
545 fp.write("%s\t%-42s\t%s\n\n" % ("Number of Reads","Name of isomir","Sequence"))
|
|
|
546 if con=="t":
|
|
|
547 fp = open('split2/'+name, 'w')
|
|
|
548 fp.write("%s\t%-42s\t%s\n\n" % ("Number of Reads","Name of isomir","Sequence"))
|
|
|
549
|
|
|
550 for i in range(len(sorted_uni_arms)):
|
|
|
551 temp = []
|
|
|
552 for j in range(len(unique_seq)):
|
|
|
553
|
|
|
554 if sorted_uni_arms[i][0] in (unique_seq[j][2].split("_")[0]+"_"+unique_seq[j][2].split("_")[1]):
|
|
|
555
|
|
|
556 temp.append(unique_seq[j])
|
|
|
557
|
|
|
558 temp = sorted(temp, key=lambda x: int(x[0].split('-')[1]), reverse=True)
|
|
|
559 fp.write("*********************************************************************************************************\n")
|
|
|
560 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]),"|"))
|
|
|
561 fp.write("*********************************************************************************************************\n\n")
|
|
|
562 [fp.write("%-8s\t%-40s\t%s\n" % (x[0].split("-")[1], x[2],x[9])) for x in temp]
|
|
|
563 fp.write("\n" + "\n")
|
|
|
564 fp.close()
|
|
|
565
|
|
|
566 if f==2:
|
|
|
567
|
|
|
568 if con=="c":
|
|
|
569 fp = open('split3/'+name, 'w')
|
|
|
570 fp.write("%s\t%-42s\t%s\n\n" % ("Number of Reads","Name of isomir","Sequence"))
|
|
|
571 if con=="t":
|
|
|
572 fp = open('split4/'+name, 'w')
|
|
|
573 fp.write("%s\t%-42s\t%s\n\n" % ("Number of Reads","Name of isomir","Sequence"))
|
|
|
574
|
|
|
575 for i in range(len(sorted_uni_arms)):
|
|
|
576 temp = []
|
|
|
577 for j in range(len(unique_seq)):
|
|
|
578 if sorted_uni_arms[i][0]==unique_seq[j][2].split("__")[0]:
|
|
|
579 temp.append(unique_seq[j])
|
|
|
580 if temp!=[]:
|
|
|
581 temp = sorted(temp, key=lambda x: int(x[0].split('-')[1]), reverse=True)
|
|
|
582 fp.write("*********************************************************************************************************\n")
|
|
|
583 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]),"|"))
|
|
|
584 fp.write("*********************************************************************************************************\n\n")
|
|
|
585 [fp.write("%-8s\t%-40s\t%s\n" % (x[0].split("-")[1], x[2],x[9])) for x in temp]
|
|
|
586 fp.write("\n" + "\n")
|
|
|
587 fp.close()
|
|
|
588
|
|
|
589
|
|
|
590 ##########################################################################################################################
|
|
|
591
|
|
|
592 def new_mat_seq(pre_unique_seq,mat_mirnas,l):
|
|
|
593
|
|
|
594 unique_iso = []
|
|
|
595 for x in pre_unique_seq:
|
|
|
596 if len(x[2].split("_"))==3:
|
|
|
597 for y in pre_unique_seq:
|
|
|
598 if x[2] in y[2] and int(x[0].split("-")[1])<int(y[0].split("-")[1]):
|
|
|
599 if any(y[2] in lst2 for lst2 in unique_iso)==False:
|
|
|
600 y[2]=">"+y[2]
|
|
|
601 unique_iso.append(y)
|
|
|
602 l.acquire()
|
|
|
603 for x in unique_iso:
|
|
|
604 mat_mirnas.append(x[2])
|
|
|
605 mat_mirnas.append(x[9])
|
|
|
606 l.release()
|
|
|
607
|
|
|
608 #########################################################################################################################
|
|
|
609
|
|
|
610 def merging_names(LH2E_copy,new):
|
|
|
611
|
|
|
612 dupes=[]
|
|
|
613 final_LH2E =[]
|
|
|
614
|
|
|
615 for num in range(len(LH2E_copy)):
|
|
|
616
|
|
|
617 if LH2E_copy[num][1] not in final_LH2E and LH2E_copy[num][0] not in final_LH2E:
|
|
|
618 final_LH2E.append(LH2E_copy[num][1])
|
|
|
619 final_LH2E.append(LH2E_copy[num][0])
|
|
|
620 else:
|
|
|
621 dupes.append(LH2E_copy[num][1])
|
|
|
622
|
|
|
623 dupes=list(set(dupes))
|
|
|
624
|
|
|
625 for i in range(len(dupes)):
|
|
|
626 dupes[i]=[dupes[i]]
|
|
|
627
|
|
|
628 for x in LH2E_copy:
|
|
|
629 for y in dupes:
|
|
|
630 if x[1]==y[0]:
|
|
|
631 fl=0
|
|
|
632 if len(y)==1:
|
|
|
633 y.append(x[0])
|
|
|
634 else:
|
|
|
635 for i in range(1,len(y)):
|
|
|
636 if y[i].split("_")[0]+"_"+y[i].split("_")[1]==x[0].split("_")[0]+"_"+x[0].split("_")[1]:
|
|
|
637 fl=1
|
|
|
638 if len(x[0])<len(y[i]):
|
|
|
639 del y[i]
|
|
|
640 y.append(x[0])
|
|
|
641 break
|
|
|
642
|
|
|
643 if fl==0:
|
|
|
644 y.append((x[0]))
|
|
|
645
|
|
|
646 for y in dupes:
|
|
|
647 if len(y)>2:
|
|
|
648 for i in range(len(y)-1,1,-1):
|
|
|
649 y[1]=y[1]+"/"+y[i]
|
|
|
650 del y[i]
|
|
|
651
|
|
|
652
|
|
|
653 for x in LH2E_copy:
|
|
|
654 for y in dupes:
|
|
|
655 if x[1]==y[0]:
|
|
|
656 x[0]=y[1]
|
|
|
657
|
|
|
658 LH2E_copy.sort()
|
|
|
659 LH2E_copy=list(LH2E_copy for LH2E_copy,_ in itertools.groupby(LH2E_copy))
|
|
|
660 new.extend(LH2E_copy)
|
|
|
661
|
|
|
662 ######################################################################################################################################################
|
|
|
663
|
|
|
664 def ssamples1(tem_names,tem_samp,non_names,non_samp,folder,pro):
|
|
|
665
|
|
|
666 for i in range(2,len(tem_samp[0])):
|
|
|
667
|
|
|
668 fp = open(folder+tem_names[i-2]+'.txt','w')
|
|
|
669 fp.write("miRNA id"+"\t"+tem_names[i-2]+"\n")
|
|
|
670
|
|
|
671 for x in tem_samp:
|
|
|
672 fp.write("%s" % "\t".join([x[0],x[i]])+"\n")
|
|
|
673
|
|
|
674 for j in range(len(non_names)):
|
|
|
675 if non_names[j]==tem_names[i-2]:
|
|
|
676 for x in non_samp:
|
|
|
677 fp.write("%s" % "\t".join([x[0],x[j+2]])+"\n")
|
|
|
678 fp.close()
|
|
|
679
|
|
|
680 #################################################################################################################################################################################################################
|
|
|
681
|
|
|
682 def download_matures(matures,org_name):
|
|
|
683
|
|
|
684 mature_mir=[]
|
|
|
685
|
|
|
686 mat_url = 'http://mirgenedb.org/fasta/'+org_name+'?mat=1'
|
|
|
687 star_url = 'http://mirgenedb.org/fasta/'+org_name+'?star=1'
|
|
|
688
|
|
|
689 data = urllib.request.urlopen(mat_url).read()
|
|
|
690 file_mirna = data.decode('utf-8')
|
|
|
691 mature_mir = file_mirna.split("\n")
|
|
|
692 mature_mir = [x.replace(">","") for x in mature_mir]
|
|
|
693 del mature_mir[-1]
|
|
|
694
|
|
|
695 data = urllib.request.urlopen(star_url).read()
|
|
|
696 file_mirna = data.decode('utf-8')
|
|
|
697 star_mir = file_mirna.split("\n")
|
|
|
698 star_mir = [x.replace(">","") for x in star_mir]
|
|
|
699 del star_mir[-1]
|
|
|
700
|
|
|
701 mature_mir.extend(star_mir)
|
|
|
702
|
|
|
703 for i in range(1,len(mature_mir),2):
|
|
|
704 mature_mir[i]=mature_mir[i].replace("U","T")
|
|
|
705
|
|
|
706 matures.extend(mature_mir)
|
|
|
707
|
|
|
708 ###################################################################################################################
|
|
|
709
|
|
|
710 def non_template_ref(sc,st,all_isoforms):
|
|
|
711
|
|
|
712 pre_uni_seq_con = list(sc)
|
|
|
713 pre_uni_seq_tre = list(st)
|
|
|
714
|
|
|
715 for x in pre_uni_seq_con:
|
|
|
716 for y in x:
|
|
|
717 if y[2] not in all_isoforms and len(y[2].split("_"))>2:
|
|
|
718 all_isoforms.append(y[2])
|
|
|
719 all_isoforms.append(y[9])
|
|
|
720
|
|
|
721 for x in pre_uni_seq_tre:
|
|
|
722 for y in x:
|
|
|
723 if y[2] not in all_isoforms and len(y[2].split("_"))>2:
|
|
|
724 all_isoforms.append(y[2])
|
|
|
725 all_isoforms.append(y[9])
|
|
|
726
|
|
|
727 ################################################################################################################################################################################################
|
|
|
728
|
|
|
729 def deseqe2(sample,mir_names,l,new_d,sample_name,sample_order):
|
|
|
730
|
|
|
731 for y in mir_names:
|
|
|
732 flag=0
|
|
|
733 for x in sample:
|
|
|
734 if y[0]==x[0]:
|
|
|
735 flag=1
|
|
|
736 break
|
|
|
737 if flag==0:
|
|
|
738 sample.append([y[0],"0",y[1]])
|
|
|
739
|
|
|
740 sample.sort(key=lambda x: x[0])
|
|
|
741 sample=list(sample for sample,_ in itertools.groupby(sample))
|
|
|
742
|
|
|
743 l.acquire()
|
|
|
744 new_d.append(sample)
|
|
|
745 sample_order.append(sample_name)
|
|
|
746 l.release()
|
|
|
747
|
|
|
748 ###############################################################################################################################################################################################
|
|
|
749
|
