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1 #!/usr/bin/env python
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2 #Guruprasad Ananda
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3 """
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4 This tool computes microsatellite mutability for the orthologous microsatellites fetched from 'Extract Orthologous Microsatellites from pair-wise alignments' tool.
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5 """
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6 import fileinput
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7 import string
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8 import sys
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9 import tempfile
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10 from galaxy.tools.util.galaxyops import *
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11 from bx.intervals.io import *
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12 from bx.intervals.operations import quicksect
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13
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14 fout = open(sys.argv[2],'w')
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15 p_group = int(sys.argv[3]) #primary "group-by" feature
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16 p_bin_size = int(sys.argv[4])
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17 s_group = int(sys.argv[5]) #sub-group by feature
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18 s_bin_size = int(sys.argv[6])
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19 mono_threshold = 9
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20 non_mono_threshold = 4
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21 p_group_cols = [p_group, p_group+7]
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22 s_group_cols = [s_group, s_group+7]
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23 num_generations = int(sys.argv[7])
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24 region = sys.argv[8]
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25 int_file = sys.argv[9]
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26 if int_file != "None": #User has specified an interval file
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27 try:
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28 fint = open(int_file, 'r')
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29 dbkey_i = sys.argv[10]
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30 chr_col_i, start_col_i, end_col_i, strand_col_i = parse_cols_arg( sys.argv[11] )
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31 except:
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32 stop_err("Unable to open input Interval file")
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33
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34
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35 def stop_err(msg):
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36 sys.stderr.write(msg)
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37 sys.exit()
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38
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39
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40 def reverse_complement(text):
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41 DNA_COMP = string.maketrans( "ACGTacgt", "TGCAtgca" )
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42 comp = [ch for ch in text.translate(DNA_COMP)]
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43 comp.reverse()
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44 return "".join(comp)
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45
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46
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47 def get_unique_elems(elems):
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48 seen = set()
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49 return[x for x in elems if x not in seen and not seen.add(x)]
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50
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51
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52 def get_binned_lists(uniqlist, binsize):
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53 binnedlist = []
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54 uniqlist.sort()
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55 start = int(uniqlist[0])
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56 bin_ind = 0
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57 l_ind = 0
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58 binnedlist.append([])
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59 while l_ind < len(uniqlist):
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60 elem = int(uniqlist[l_ind])
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61 if elem in range(start, start+binsize):
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62 binnedlist[bin_ind].append(elem)
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63 else:
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64 start += binsize
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65 bin_ind += 1
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66 binnedlist.append([])
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67 binnedlist[bin_ind].append(elem)
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68 l_ind += 1
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69 return binnedlist
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70
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71
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72 def fetch_weight(H, C, t):
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73 if (H-(C-H)) < t:
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74 return 2.0
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75 else:
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76 return 1.0
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77
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78
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79 def mutabilityEstimator(repeats1, repeats2, thresholds):
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80 mut_num = 0.0 #Mutability Numerator
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81 mut_den = 0.0 #Mutability denominator
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82 for ind, H in enumerate(repeats1):
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83 C = repeats2[ind]
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84 t = thresholds[ind]
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85 w = fetch_weight(H, C, t)
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86 mut_num += ((H-C)*(H-C)*w)
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87 mut_den += w
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88 return [mut_num, mut_den]
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89
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90
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91 def output_writer(blk, blk_lines):
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92 global winspecies, speciesind
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93 all_elems_1 = []
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94 all_elems_2 = []
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95 all_s_elems_1 = []
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96 all_s_elems_2 = []
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97 for bline in blk_lines:
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98 if not(bline):
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99 continue
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100 items = bline.split('\t')
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101 seq1 = items[1]
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102 seq2 = items[8]
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103 if p_group_cols[0] == 6:
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104 items[p_group_cols[0]] = int(items[p_group_cols[0]])
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105 items[p_group_cols[1]] = int(items[p_group_cols[1]])
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106 if s_group_cols[0] == 6:
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107 items[s_group_cols[0]] = int(items[s_group_cols[0]])
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108 items[s_group_cols[1]] = int(items[s_group_cols[1]])
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109 all_elems_1.append(items[p_group_cols[0]]) #primary col elements for species 1
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110 all_elems_2.append(items[p_group_cols[1]]) #primary col elements for species 2
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111 if s_group_cols[0] != -1: #sub-group is not None
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112 all_s_elems_1.append(items[s_group_cols[0]]) #secondary col elements for species 1
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113 all_s_elems_2.append(items[s_group_cols[1]]) #secondary col elements for species 2
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114 uniq_elems_1 = get_unique_elems(all_elems_1)
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115 uniq_elems_2 = get_unique_elems(all_elems_2)
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116 if s_group_cols[0] != -1:
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117 uniq_s_elems_1 = get_unique_elems(all_s_elems_1)
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118 uniq_s_elems_2 = get_unique_elems(all_s_elems_2)
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119 mut1 = {}
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120 mut2 = {}
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121 count1 = {}
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122 count2 = {}
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123 """
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124 if p_group_cols[0] == 7: #i.e. the option chosen is group-by unit(AG, GTC, etc)
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125 uniq_elems_1 = get_unique_units(j.sort(lambda x, y: len(x)-len(y)))
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126 """
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127 if p_group_cols[0] == 6: #i.e. the option chosen is group-by repeat number.
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128 uniq_elems_1 = get_binned_lists( uniq_elems_1, p_bin_size )
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129 uniq_elems_2 = get_binned_lists( uniq_elems_2, p_bin_size )
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130
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131 if s_group_cols[0] == 6: #i.e. the option chosen is subgroup-by repeat number.
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132 uniq_s_elems_1 = get_binned_lists( uniq_s_elems_1, s_bin_size )
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133 uniq_s_elems_2 = get_binned_lists( uniq_s_elems_2, s_bin_size )
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134
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135 for pitem1 in uniq_elems_1:
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136 #repeats1 = []
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137 #repeats2 = []
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138 thresholds = []
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139 if s_group_cols[0] != -1: #Sub-group by feature is not None
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140 for sitem1 in uniq_s_elems_1:
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141 repeats1 = []
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142 repeats2 = []
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143 if type(sitem1) == type(''):
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144 sitem1 = sitem1.strip()
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145 for bline in blk_lines:
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146 belems = bline.split('\t')
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147 if type(pitem1) == list:
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148 if p_group_cols[0] == 6:
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149 belems[p_group_cols[0]] = int(belems[p_group_cols[0]])
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150 if belems[p_group_cols[0]] in pitem1:
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151 if belems[s_group_cols[0]] == sitem1:
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152 repeats1.append(int(belems[6]))
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153 repeats2.append(int(belems[13]))
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154 if belems[4] == 'mononucleotide':
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155 thresholds.append(mono_threshold)
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156 else:
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157 thresholds.append(non_mono_threshold)
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158 mut1[str(pitem1)+'\t'+str(sitem1)] = mutabilityEstimator( repeats1, repeats2, thresholds )
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159 if region == 'align':
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160 count1[str(pitem1)+'\t'+str(sitem1)] = min( sum(repeats1), sum(repeats2) )
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161 else:
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162 if winspecies == 1:
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163 count1["%s\t%s" % ( pitem1, sitem1 )] = sum(repeats1)
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164 elif winspecies == 2:
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165 count1["%s\t%s" % ( pitem1, sitem1 )] = sum(repeats2)
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166 else:
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167 if type(sitem1) == list:
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168 if s_group_cols[0] == 6:
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169 belems[s_group_cols[0]] = int(belems[s_group_cols[0]])
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170 if belems[p_group_cols[0]] == pitem1 and belems[s_group_cols[0]] in sitem1:
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171 repeats1.append(int(belems[6]))
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172 repeats2.append(int(belems[13]))
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173 if belems[4] == 'mononucleotide':
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174 thresholds.append(mono_threshold)
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175 else:
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176 thresholds.append(non_mono_threshold)
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177 mut1["%s\t%s" % ( pitem1, sitem1 )] = mutabilityEstimator( repeats1, repeats2, thresholds )
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178 if region == 'align':
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179 count1[str(pitem1)+'\t'+str(sitem1)] = min( sum(repeats1), sum(repeats2) )
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180 else:
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181 if winspecies == 1:
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182 count1[str(pitem1)+'\t'+str(sitem1)] = sum(repeats1)
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183 elif winspecies == 2:
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184 count1[str(pitem1)+'\t'+str(sitem1)] = sum(repeats2)
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185 else:
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186 if belems[p_group_cols[0]] == pitem1 and belems[s_group_cols[0]] == sitem1:
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187 repeats1.append(int(belems[6]))
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188 repeats2.append(int(belems[13]))
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189 if belems[4] == 'mononucleotide':
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190 thresholds.append(mono_threshold)
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191 else:
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192 thresholds.append(non_mono_threshold)
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193 mut1["%s\t%s" % ( pitem1, sitem1 )] = mutabilityEstimator( repeats1, repeats2, thresholds )
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194 if region == 'align':
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195 count1[str(pitem1)+'\t'+str(sitem1)] = min( sum(repeats1), sum(repeats2) )
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196 else:
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197 if winspecies == 1:
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198 count1["%s\t%s" % ( pitem1, sitem1 )] = sum(repeats1)
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199 elif winspecies == 2:
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200 count1["%s\t%s" % ( pitem1, sitem1 )] = sum(repeats2)
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201 else: #Sub-group by feature is None
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202 for bline in blk_lines:
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203 belems = bline.split('\t')
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204 if type(pitem1) == list:
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205 #print >> sys.stderr, "item: " + str(item1)
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206 if p_group_cols[0] == 6:
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207 belems[p_group_cols[0]] = int(belems[p_group_cols[0]])
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208 if belems[p_group_cols[0]] in pitem1:
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209 repeats1.append(int(belems[6]))
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210 repeats2.append(int(belems[13]))
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211 if belems[4] == 'mononucleotide':
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212 thresholds.append(mono_threshold)
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213 else:
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214 thresholds.append(non_mono_threshold)
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215 else:
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216 if belems[p_group_cols[0]] == pitem1:
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217 repeats1.append(int(belems[6]))
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218 repeats2.append(int(belems[13]))
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219 if belems[4] == 'mononucleotide':
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220 thresholds.append(mono_threshold)
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221 else:
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222 thresholds.append(non_mono_threshold)
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223 mut1["%s" % (pitem1)] = mutabilityEstimator( repeats1, repeats2, thresholds )
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224 if region == 'align':
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225 count1["%s" % (pitem1)] = min( sum(repeats1), sum(repeats2) )
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226 else:
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227 if winspecies == 1:
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228 count1[str(pitem1)] = sum(repeats1)
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229 elif winspecies == 2:
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230 count1[str(pitem1)] = sum(repeats2)
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231
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232 for pitem2 in uniq_elems_2:
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233 #repeats1 = []
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234 #repeats2 = []
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235 thresholds = []
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236 if s_group_cols[0] != -1: #Sub-group by feature is not None
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237 for sitem2 in uniq_s_elems_2:
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238 repeats1 = []
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239 repeats2 = []
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240 if type(sitem2)==type(''):
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241 sitem2 = sitem2.strip()
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242 for bline in blk_lines:
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243 belems = bline.split('\t')
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244 if type(pitem2) == list:
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245 if p_group_cols[0] == 6:
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246 belems[p_group_cols[1]] = int(belems[p_group_cols[1]])
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247 if belems[p_group_cols[1]] in pitem2 and belems[s_group_cols[1]] == sitem2:
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248 repeats2.append(int(belems[13]))
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249 repeats1.append(int(belems[6]))
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250 if belems[4] == 'mononucleotide':
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251 thresholds.append(mono_threshold)
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252 else:
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253 thresholds.append(non_mono_threshold)
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254 mut2["%s\t%s" % ( pitem2, sitem2 )] = mutabilityEstimator( repeats2, repeats1, thresholds )
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255 #count2[str(pitem2)+'\t'+str(sitem2)]=len(repeats2)
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256 if region == 'align':
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257 count2["%s\t%s" % ( pitem2, sitem2 )] = min( sum(repeats1), sum(repeats2) )
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258 else:
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259 if winspecies == 1:
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260 count2["%s\t%s" % ( pitem2, sitem2 )] = len(repeats2)
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261 elif winspecies == 2:
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262 count2["%s\t%s" % ( pitem2, sitem2 )] = len(repeats1)
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263 else:
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264 if type(sitem2) == list:
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265 if s_group_cols[0] == 6:
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266 belems[s_group_cols[1]] = int(belems[s_group_cols[1]])
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267 if belems[p_group_cols[1]] == pitem2 and belems[s_group_cols[1]] in sitem2:
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268 repeats2.append(int(belems[13]))
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269 repeats1.append(int(belems[6]))
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270 if belems[4] == 'mononucleotide':
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271 thresholds.append(mono_threshold)
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272 else:
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273 thresholds.append(non_mono_threshold)
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274 mut2["%s\t%s" % ( pitem2, sitem2 )] = mutabilityEstimator( repeats2, repeats1, thresholds )
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275 if region == 'align':
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276 count2["%s\t%s" % ( pitem2, sitem2 )] = min( sum(repeats1), sum(repeats2) )
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277 else:
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278 if winspecies == 1:
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279 count2["%s\t%s" % ( pitem2, sitem2 )] = len(repeats2)
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280 elif winspecies == 2:
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281 count2["%s\t%s" % ( pitem2, sitem2 )] = len(repeats1)
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282 else:
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283 if belems[p_group_cols[1]] == pitem2 and belems[s_group_cols[1]] == sitem2:
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284 repeats1.append(int(belems[13]))
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285 repeats2.append(int(belems[6]))
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286 if belems[4] == 'mononucleotide':
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287 thresholds.append(mono_threshold)
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288 else:
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289 thresholds.append(non_mono_threshold)
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290 mut2["%s\t%s" % ( pitem2, sitem2 )] = mutabilityEstimator( repeats2, repeats1, thresholds )
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291 if region == 'align':
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292 count2["%s\t%s" % ( pitem2, sitem2 )] = min( sum(repeats1), sum(repeats2) )
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293 else:
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294 if winspecies == 1:
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295 count2["%s\t%s" % ( pitem2, sitem2 )] = len(repeats2)
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296 elif winspecies == 2:
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297 count2["%s\t%s" % ( pitem2, sitem2 )] = len(repeats1)
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298 else: #Sub-group by feature is None
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299 for bline in blk_lines:
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300 belems = bline.split('\t')
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301 if type(pitem2) == list:
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302 if p_group_cols[0] == 6:
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303 belems[p_group_cols[1]] = int(belems[p_group_cols[1]])
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304 if belems[p_group_cols[1]] in pitem2:
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305 repeats2.append(int(belems[13]))
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306 repeats1.append(int(belems[6]))
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307 if belems[4] == 'mononucleotide':
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308 thresholds.append(mono_threshold)
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309 else:
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310 thresholds.append(non_mono_threshold)
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311 else:
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312 if belems[p_group_cols[1]] == pitem2:
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313 repeats2.append(int(belems[13]))
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314 repeats1.append(int(belems[6]))
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315 if belems[4] == 'mononucleotide':
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316 thresholds.append(mono_threshold)
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317 else:
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318 thresholds.append(non_mono_threshold)
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319 mut2["%s" % (pitem2)] = mutabilityEstimator( repeats2, repeats1, thresholds )
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320 if region == 'align':
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321 count2["%s" % (pitem2)] = min( sum(repeats1), sum(repeats2) )
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322 else:
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323 if winspecies == 1:
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324 count2["%s" % (pitem2)] = sum(repeats2)
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325 elif winspecies == 2:
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326 count2["%s" % (pitem2)] = sum(repeats1)
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327 for key in mut1.keys():
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328 if key in mut2.keys():
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329 mut = (mut1[key][0]+mut2[key][0])/(mut1[key][1]+mut2[key][1])
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330 count = count1[key]
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331 del mut2[key]
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332 else:
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333 unit_found = False
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334 if p_group_cols[0] == 7 or s_group_cols[0] == 7: #if it is Repeat Unit (AG, GCT etc.) check for reverse-complements too
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335 if p_group_cols[0] == 7:
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336 this, other = 0, 1
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337 else:
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338 this, other = 1, 0
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339 groups1 = key.split('\t')
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340 mutn = mut1[key][0]
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341 mutd = mut1[key][1]
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342 count = 0
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343 for key2 in mut2.keys():
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344 groups2 = key2.split('\t')
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345 if groups1[other] == groups2[other]:
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346 if groups1[this] in groups2[this]*2 or reverse_complement(groups1[this]) in groups2[this]*2:
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347 #mut = (mut1[key][0]+mut2[key2][0])/(mut1[key][1]+mut2[key2][1])
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348 mutn += mut2[key2][0]
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349 mutd += mut2[key2][1]
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350 count += int(count2[key2])
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351 unit_found = True
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352 del mut2[key2]
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353 #break
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354 if unit_found:
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355 mut = mutn/mutd
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356 else:
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357 mut = mut1[key][0]/mut1[key][1]
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358 count = count1[key]
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359 mut = "%.2e" % (mut/num_generations)
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360 if region == 'align':
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361 print >> fout, str(blk) + '\t'+seq1 + '\t' + seq2 + '\t' +key.strip()+ '\t'+str(mut) + '\t'+ str(count)
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362 elif region == 'win':
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363 fout.write("%s\t%s\t%s\t%s\n" % ( blk, key.strip(), mut, count ))
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364 fout.flush()
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365
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366 #catch any remaining repeats, for instance if the orthologous position contained different repeat units
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367 for remaining_key in mut2.keys():
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368 mut = mut2[remaining_key][0]/mut2[remaining_key][1]
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369 mut = "%.2e" % (mut/num_generations)
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370 count = count2[remaining_key]
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371 if region == 'align':
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372 print >> fout, str(blk) + '\t'+seq1 + '\t'+seq2 + '\t'+remaining_key.strip()+ '\t'+str(mut)+ '\t'+ str(count)
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373 elif region == 'win':
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374 fout.write("%s\t%s\t%s\t%s\n" % ( blk, remaining_key.strip(), mut, count ))
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375 fout.flush()
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376 #print >> fout, blk + '\t'+remaining_key.strip()+ '\t'+str(mut)+ '\t'+ str(count)
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377
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378
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379 def counter(node, start, end, report_func):
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380 if start <= node.start < end and start < node.end <= end:
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381 report_func(node)
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382 if node.right:
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383 counter(node.right, start, end, report_func)
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384 if node.left:
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385 counter(node.left, start, end, report_func)
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386 elif node.start < start and node.right:
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387 counter(node.right, start, end, report_func)
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|
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388 elif node.start >= end and node.left and node.left.maxend > start:
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389 counter(node.left, start, end, report_func)
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|
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390
|
|
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391
|
|
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392 def main():
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393 infile = sys.argv[1]
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394
|
|
|
395 for i, line in enumerate( file ( infile )):
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396 line = line.rstrip('\r\n')
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|
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397 if len( line )>0 and not line.startswith( '#' ):
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|
|
398 elems = line.split( '\t' )
|
|
|
399 break
|
|
|
400 if i == 30:
|
|
|
401 break # Hopefully we'll never get here...
|
|
|
402
|
|
|
403 if len( elems ) != 15:
|
|
|
404 stop_err( "This tool only works on tabular data output by 'Extract Orthologous Microsatellites from pair-wise alignments' tool. The data in your input dataset is either missing or not formatted properly." )
|
|
|
405 global winspecies, speciesind
|
|
|
406 if region == 'win':
|
|
|
407 if dbkey_i in elems[1]:
|
|
|
408 winspecies = 1
|
|
|
409 speciesind = 1
|
|
|
410 elif dbkey_i in elems[8]:
|
|
|
411 winspecies = 2
|
|
|
412 speciesind = 8
|
|
|
413 else:
|
|
|
414 stop_err("The species build corresponding to your interval file is not present in the Microsatellite file.")
|
|
|
415
|
|
|
416 fin = open(infile, 'r')
|
|
|
417 skipped = 0
|
|
|
418 linestr = ""
|
|
|
419
|
|
|
420 if region == 'win':
|
|
|
421 msats = NiceReaderWrapper( fileinput.FileInput( infile ),
|
|
|
422 chrom_col = speciesind,
|
|
|
423 start_col = speciesind+1,
|
|
|
424 end_col = speciesind+2,
|
|
|
425 strand_col = -1,
|
|
|
426 fix_strand = True)
|
|
|
427 msatTree = quicksect.IntervalTree()
|
|
|
428 for item in msats:
|
|
|
429 if type( item ) is GenomicInterval:
|
|
|
430 msatTree.insert( item, msats.linenum, item.fields )
|
|
|
431
|
|
|
432 for iline in fint:
|
|
|
433 try:
|
|
|
434 iline = iline.rstrip('\r\n')
|
|
|
435 if not(iline) or iline == "":
|
|
|
436 continue
|
|
|
437 ielems = iline.strip("\r\n").split('\t')
|
|
|
438 ichr = ielems[chr_col_i]
|
|
|
439 istart = int(ielems[start_col_i])
|
|
|
440 iend = int(ielems[end_col_i])
|
|
|
441 isrc = "%s.%s" % ( dbkey_i, ichr )
|
|
|
442 if isrc not in msatTree.chroms:
|
|
|
443 continue
|
|
|
444 result = []
|
|
|
445 root = msatTree.chroms[isrc] #root node for the chrom
|
|
|
446 counter(root, istart, iend, lambda node: result.append( node ))
|
|
|
447 if not(result):
|
|
|
448 continue
|
|
|
449 tmpfile1 = tempfile.NamedTemporaryFile('wb+')
|
|
|
450 for node in result:
|
|
|
451 tmpfile1.write("%s\n" % "\t".join( node.other ))
|
|
|
452
|
|
|
453 tmpfile1.seek(0)
|
|
|
454 output_writer(iline, tmpfile1.readlines())
|
|
|
455 except:
|
|
|
456 skipped += 1
|
|
|
457 if skipped:
|
|
|
458 print "Skipped %d intervals as invalid." % (skipped)
|
|
|
459 elif region == 'align':
|
|
|
460 if s_group_cols[0] != -1:
|
|
|
461 print >> fout, "#Window\tSpecies_1\tSpecies_2\tGroupby_Feature\tSubGroupby_Feature\tMutability\tCount"
|
|
|
462 else:
|
|
|
463 print >> fout, "#Window\tSpecies_1\tWindow_Start\tWindow_End\tSpecies_2\tGroupby_Feature\tMutability\tCount"
|
|
|
464 prev_bnum = -1
|
|
|
465 try:
|
|
|
466 for line in fin:
|
|
|
467 line = line.strip("\r\n")
|
|
|
468 if not(line) or line == "":
|
|
|
469 continue
|
|
|
470 elems = line.split('\t')
|
|
|
471 try:
|
|
|
472 assert int(elems[0])
|
|
|
473 assert len(elems) == 15
|
|
|
474 except:
|
|
|
475 continue
|
|
|
476 new_bnum = int(elems[0])
|
|
|
477 if new_bnum != prev_bnum:
|
|
|
478 if prev_bnum != -1:
|
|
|
479 output_writer(prev_bnum, linestr.strip().replace('\r','\n').split('\n'))
|
|
|
480 linestr = line + "\n"
|
|
|
481 else:
|
|
|
482 linestr += line
|
|
|
483 linestr += "\n"
|
|
|
484 prev_bnum = new_bnum
|
|
|
485 output_writer(prev_bnum, linestr.strip().replace('\r','\n').split('\n'))
|
|
|
486 except Exception, ea:
|
|
|
487 print >> sys.stderr, ea
|
|
|
488 skipped += 1
|
|
|
489 if skipped:
|
|
|
490 print "Skipped %d lines as invalid." % (skipped)
|
|
|
491
|
|
|
492
|
|
|
493 if __name__ == "__main__":
|
|
|
494 main()
|
