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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 from galaxy import eggs
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7 import sys, string, re, commands, tempfile, os, fileinput
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8 from galaxy.tools.util.galaxyops import *
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9 from bx.intervals.io import *
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10 from bx.intervals.operations import quicksect
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11
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12 fout = open(sys.argv[2],'w')
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13 p_group = int(sys.argv[3]) #primary "group-by" feature
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14 p_bin_size = int(sys.argv[4])
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15 s_group = int(sys.argv[5]) #sub-group by feature
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16 s_bin_size = int(sys.argv[6])
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17 mono_threshold = 9
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18 non_mono_threshold = 4
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19 p_group_cols = [p_group, p_group+7]
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20 s_group_cols = [s_group, s_group+7]
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21 num_generations = int(sys.argv[7])
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22 region = sys.argv[8]
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23 int_file = sys.argv[9]
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24 if int_file != "None": #User has specified an interval file
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25 try:
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26 fint = open(int_file, 'r')
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27 dbkey_i = sys.argv[10]
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28 chr_col_i, start_col_i, end_col_i, strand_col_i = parse_cols_arg( sys.argv[11] )
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29 except:
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30 stop_err("Unable to open input Interval file")
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31
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32 def stop_err(msg):
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33 sys.stderr.write(msg)
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34 sys.exit()
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35
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36 def reverse_complement(text):
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37 DNA_COMP = string.maketrans( "ACGTacgt", "TGCAtgca" )
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38 comp = [ch for ch in text.translate(DNA_COMP)]
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39 comp.reverse()
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40 return "".join(comp)
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41
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42 def get_unique_elems(elems):
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43 seen=set()
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44 return[x for x in elems if x not in seen and not seen.add(x)]
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45
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46 def get_binned_lists(uniqlist, binsize):
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47 binnedlist=[]
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48 uniqlist.sort()
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49 start = int(uniqlist[0])
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50 bin_ind=0
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51 l_ind=0
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52 binnedlist.append([])
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53 while l_ind < len(uniqlist):
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54 elem = int(uniqlist[l_ind])
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55 if elem in range(start,start+binsize):
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56 binnedlist[bin_ind].append(elem)
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57 else:
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58 start += binsize
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59 bin_ind += 1
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60 binnedlist.append([])
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61 binnedlist[bin_ind].append(elem)
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62 l_ind += 1
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63 return binnedlist
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64
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65 def fetch_weight(H,C,t):
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66 if (H-(C-H)) < t:
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67 return 2.0
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68 else:
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69 return 1.0
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70
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71 def mutabilityEstimator(repeats1,repeats2,thresholds):
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72 mut_num = 0.0 #Mutability Numerator
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73 mut_den = 0.0 #Mutability denominator
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74 for ind,H in enumerate(repeats1):
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75 C = repeats2[ind]
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76 t = thresholds[ind]
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77 w = fetch_weight(H,C,t)
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78 mut_num += ((H-C)*(H-C)*w)
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79 mut_den += w
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80 return [mut_num, mut_den]
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81
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82 def output_writer(blk, blk_lines):
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83 global winspecies, speciesind
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84 all_elems_1=[]
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85 all_elems_2=[]
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86 all_s_elems_1=[]
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87 all_s_elems_2=[]
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88 for bline in blk_lines:
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89 if not(bline):
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90 continue
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91 items = bline.split('\t')
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92 seq1 = items[1]
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93 start1 = items[2]
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94 end1 = items[3]
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95 seq2 = items[8]
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96 start2 = items[9]
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97 end2 = items[10]
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98 if p_group_cols[0] == 6:
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99 items[p_group_cols[0]] = int(items[p_group_cols[0]])
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100 items[p_group_cols[1]] = int(items[p_group_cols[1]])
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101 if s_group_cols[0] == 6:
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102 items[s_group_cols[0]] = int(items[s_group_cols[0]])
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103 items[s_group_cols[1]] = int(items[s_group_cols[1]])
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104 all_elems_1.append(items[p_group_cols[0]]) #primary col elements for species 1
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105 all_elems_2.append(items[p_group_cols[1]]) #primary col elements for species 2
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106 if s_group_cols[0] != -1: #sub-group is not None
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107 all_s_elems_1.append(items[s_group_cols[0]]) #secondary col elements for species 1
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108 all_s_elems_2.append(items[s_group_cols[1]]) #secondary col elements for species 2
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109 uniq_elems_1 = get_unique_elems(all_elems_1)
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110 uniq_elems_2 = get_unique_elems(all_elems_2)
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111 if s_group_cols[0] != -1:
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112 uniq_s_elems_1 = get_unique_elems(all_s_elems_1)
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113 uniq_s_elems_2 = get_unique_elems(all_s_elems_2)
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114 mut1={}
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115 mut2={}
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116 count1 = {}
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117 count2 = {}
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118 """
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119 if p_group_cols[0] == 7: #i.e. the option chosen is group-by unit(AG, GTC, etc)
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120 uniq_elems_1 = get_unique_units(j.sort(lambda x, y: len(x)-len(y)))
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121 """
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122 if p_group_cols[0] == 6: #i.e. the option chosen is group-by repeat number.
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123 uniq_elems_1 = get_binned_lists(uniq_elems_1,p_bin_size)
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124 uniq_elems_2 = get_binned_lists(uniq_elems_2,p_bin_size)
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125
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126 if s_group_cols[0] == 6: #i.e. the option chosen is subgroup-by repeat number.
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127 uniq_s_elems_1 = get_binned_lists(uniq_s_elems_1,s_bin_size)
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128 uniq_s_elems_2 = get_binned_lists(uniq_s_elems_2,s_bin_size)
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129
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130 for pitem1 in uniq_elems_1:
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131 #repeats1 = []
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132 #repeats2 = []
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133 thresholds = []
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134 if s_group_cols[0] != -1: #Sub-group by feature is not None
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135 for sitem1 in uniq_s_elems_1:
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136 repeats1 = []
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137 repeats2 = []
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138 if type(sitem1) == type(''):
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139 sitem1 = sitem1.strip()
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140 for bline in blk_lines:
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141 belems = bline.split('\t')
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142 if type(pitem1) == list:
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143 if p_group_cols[0] == 6:
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144 belems[p_group_cols[0]] = int(belems[p_group_cols[0]])
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145 if belems[p_group_cols[0]] in pitem1:
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146 if belems[s_group_cols[0]]==sitem1:
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147 repeats1.append(int(belems[6]))
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148 repeats2.append(int(belems[13]))
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149 if belems[4] == 'mononucleotide':
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150 thresholds.append(mono_threshold)
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151 else:
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152 thresholds.append(non_mono_threshold)
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153 mut1[str(pitem1)+'\t'+str(sitem1)]=mutabilityEstimator(repeats1,repeats2,thresholds)
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154 if region == 'align':
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155 count1[str(pitem1)+'\t'+str(sitem1)]=min(sum(repeats1),sum(repeats2))
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156 else:
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157 if winspecies == 1:
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158 count1["%s\t%s" %(pitem1,sitem1)]=sum(repeats1)
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159 elif winspecies == 2:
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160 count1["%s\t%s" %(pitem1,sitem1)]=sum(repeats2)
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161 else:
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162 if type(sitem1) == list:
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163 if s_group_cols[0] == 6:
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164 belems[s_group_cols[0]] = int(belems[s_group_cols[0]])
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165 if belems[p_group_cols[0]]==pitem1 and belems[s_group_cols[0]] in sitem1:
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166 repeats1.append(int(belems[6]))
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167 repeats2.append(int(belems[13]))
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168 if belems[4] == 'mononucleotide':
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169 thresholds.append(mono_threshold)
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170 else:
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171 thresholds.append(non_mono_threshold)
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172 mut1["%s\t%s" %(pitem1,sitem1)]=mutabilityEstimator(repeats1,repeats2,thresholds)
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173 if region == 'align':
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174 count1[str(pitem1)+'\t'+str(sitem1)]=min(sum(repeats1),sum(repeats2))
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175 else:
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176 if winspecies == 1:
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177 count1[str(pitem1)+'\t'+str(sitem1)]=sum(repeats1)
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178 elif winspecies == 2:
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179 count1[str(pitem1)+'\t'+str(sitem1)]=sum(repeats2)
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180 else:
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181 if belems[p_group_cols[0]]==pitem1 and belems[s_group_cols[0]]==sitem1:
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182 repeats1.append(int(belems[6]))
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183 repeats2.append(int(belems[13]))
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184 if belems[4] == 'mononucleotide':
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185 thresholds.append(mono_threshold)
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186 else:
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187 thresholds.append(non_mono_threshold)
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188 mut1["%s\t%s" %(pitem1,sitem1)]=mutabilityEstimator(repeats1,repeats2,thresholds)
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189 if region == 'align':
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190 count1[str(pitem1)+'\t'+str(sitem1)]=min(sum(repeats1),sum(repeats2))
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191 else:
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192 if winspecies == 1:
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193 count1["%s\t%s" %(pitem1,sitem1)]=sum(repeats1)
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194 elif winspecies == 2:
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195 count1["%s\t%s" %(pitem1,sitem1)]=sum(repeats2)
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196 else: #Sub-group by feature is None
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197 for bline in blk_lines:
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198 belems = bline.split('\t')
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199 if type(pitem1) == list:
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200 #print >>sys.stderr, "item: " + str(item1)
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201 if p_group_cols[0] == 6:
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202 belems[p_group_cols[0]] = int(belems[p_group_cols[0]])
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203 if belems[p_group_cols[0]] in pitem1:
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204 repeats1.append(int(belems[6]))
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205 repeats2.append(int(belems[13]))
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206 if belems[4] == 'mononucleotide':
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207 thresholds.append(mono_threshold)
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208 else:
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209 thresholds.append(non_mono_threshold)
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210 else:
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211 if belems[p_group_cols[0]]==pitem1:
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212 repeats1.append(int(belems[6]))
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213 repeats2.append(int(belems[13]))
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214 if belems[4] == 'mononucleotide':
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215 thresholds.append(mono_threshold)
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216 else:
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217 thresholds.append(non_mono_threshold)
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218 mut1["%s" %(pitem1)]=mutabilityEstimator(repeats1,repeats2,thresholds)
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219 if region == 'align':
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220 count1["%s" %(pitem1)]=min(sum(repeats1),sum(repeats2))
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221 else:
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222 if winspecies == 1:
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223 count1[str(pitem1)]=sum(repeats1)
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224 elif winspecies == 2:
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225 count1[str(pitem1)]=sum(repeats2)
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226
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227 for pitem2 in uniq_elems_2:
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228 #repeats1 = []
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229 #repeats2 = []
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230 thresholds = []
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231 if s_group_cols[0] != -1: #Sub-group by feature is not None
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232 for sitem2 in uniq_s_elems_2:
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233 repeats1 = []
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234 repeats2 = []
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235 if type(sitem2)==type(''):
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236 sitem2 = sitem2.strip()
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237 for bline in blk_lines:
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238 belems = bline.split('\t')
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239 if type(pitem2) == list:
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240 if p_group_cols[0] == 6:
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241 belems[p_group_cols[1]] = int(belems[p_group_cols[1]])
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242 if belems[p_group_cols[1]] in pitem2 and belems[s_group_cols[1]]==sitem2:
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243 repeats2.append(int(belems[13]))
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244 repeats1.append(int(belems[6]))
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245 if belems[4] == 'mononucleotide':
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246 thresholds.append(mono_threshold)
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247 else:
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248 thresholds.append(non_mono_threshold)
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249 mut2["%s\t%s" %(pitem2,sitem2)]=mutabilityEstimator(repeats2,repeats1,thresholds)
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250 #count2[str(pitem2)+'\t'+str(sitem2)]=len(repeats2)
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251 if region == 'align':
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252 count2["%s\t%s" %(pitem2,sitem2)]=min(sum(repeats1),sum(repeats2))
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253 else:
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254 if winspecies == 1:
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255 count2["%s\t%s" %(pitem2,sitem2)]=len(repeats2)
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256 elif winspecies == 2:
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257 count2["%s\t%s" %(pitem2,sitem2)]=len(repeats1)
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258 else:
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259 if type(sitem2) == list:
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260 if s_group_cols[0] == 6:
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261 belems[s_group_cols[1]] = int(belems[s_group_cols[1]])
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262 if belems[p_group_cols[1]]==pitem2 and belems[s_group_cols[1]] in sitem2:
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263 repeats2.append(int(belems[13]))
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264 repeats1.append(int(belems[6]))
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265 if belems[4] == 'mononucleotide':
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266 thresholds.append(mono_threshold)
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267 else:
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268 thresholds.append(non_mono_threshold)
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269 mut2["%s\t%s" %(pitem2,sitem2)]=mutabilityEstimator(repeats2,repeats1,thresholds)
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270 if region == 'align':
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271 count2["%s\t%s" %(pitem2,sitem2)]=min(sum(repeats1),sum(repeats2))
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272 else:
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273 if winspecies == 1:
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274 count2["%s\t%s" %(pitem2,sitem2)]=len(repeats2)
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275 elif winspecies == 2:
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276 count2["%s\t%s" %(pitem2,sitem2)]=len(repeats1)
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277 else:
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278 if belems[p_group_cols[1]]==pitem2 and belems[s_group_cols[1]]==sitem2:
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279 repeats1.append(int(belems[13]))
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280 repeats2.append(int(belems[6]))
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281 if belems[4] == 'mononucleotide':
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282 thresholds.append(mono_threshold)
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283 else:
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284 thresholds.append(non_mono_threshold)
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285 mut2["%s\t%s" %(pitem2,sitem2)]=mutabilityEstimator(repeats2,repeats1,thresholds)
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286 if region == 'align':
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287 count2["%s\t%s" %(pitem2,sitem2)]=min(sum(repeats1),sum(repeats2))
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288 else:
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289 if winspecies == 1:
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290 count2["%s\t%s" %(pitem2,sitem2)]=len(repeats2)
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291 elif winspecies == 2:
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292 count2["%s\t%s" %(pitem2,sitem2)]=len(repeats1)
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293 else: #Sub-group by feature is None
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294 for bline in blk_lines:
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295 belems = bline.split('\t')
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296 if type(pitem2) == list:
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297 if p_group_cols[0] == 6:
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298 belems[p_group_cols[1]] = int(belems[p_group_cols[1]])
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299 if belems[p_group_cols[1]] in pitem2:
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300 repeats2.append(int(belems[13]))
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301 repeats1.append(int(belems[6]))
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302 if belems[4] == 'mononucleotide':
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303 thresholds.append(mono_threshold)
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304 else:
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305 thresholds.append(non_mono_threshold)
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306 else:
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307 if belems[p_group_cols[1]]==pitem2:
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308 repeats2.append(int(belems[13]))
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309 repeats1.append(int(belems[6]))
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310 if belems[4] == 'mononucleotide':
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311 thresholds.append(mono_threshold)
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312 else:
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313 thresholds.append(non_mono_threshold)
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314 mut2["%s" %(pitem2)]=mutabilityEstimator(repeats2,repeats1,thresholds)
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315 if region == 'align':
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316 count2["%s" %(pitem2)]=min(sum(repeats1),sum(repeats2))
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317 else:
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318 if winspecies == 1:
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319 count2["%s" %(pitem2)]=sum(repeats2)
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320 elif winspecies == 2:
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321 count2["%s" %(pitem2)]=sum(repeats1)
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322 for key in mut1.keys():
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323 if key in mut2.keys():
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324 mut = (mut1[key][0]+mut2[key][0])/(mut1[key][1]+mut2[key][1])
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325 count = count1[key]
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326 del mut2[key]
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327 else:
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328 unit_found = False
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329 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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330 if p_group_cols[0] == 7:
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331 this,other = 0,1
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332 else:
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333 this,other = 1,0
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334 groups1 = key.split('\t')
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335 mutn = mut1[key][0]
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336 mutd = mut1[key][1]
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337 count = 0
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338 for key2 in mut2.keys():
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339 groups2 = key2.split('\t')
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340 if groups1[other] == groups2[other]:
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341 if groups1[this] in groups2[this]*2 or reverse_complement(groups1[this]) in groups2[this]*2:
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342 #mut = (mut1[key][0]+mut2[key2][0])/(mut1[key][1]+mut2[key2][1])
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343 mutn += mut2[key2][0]
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344 mutd += mut2[key2][1]
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345 count += int(count2[key2])
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346 unit_found = True
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347 del mut2[key2]
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348 #break
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349 if unit_found:
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350 mut = mutn/mutd
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351 else:
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352 mut = mut1[key][0]/mut1[key][1]
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353 count = count1[key]
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354 mut = "%.2e" %(mut/num_generations)
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355 if region == 'align':
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356 print >>fout, str(blk) + '\t'+seq1 + '\t' + seq2 + '\t' +key.strip()+ '\t'+str(mut) + '\t'+ str(count)
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357 elif region == 'win':
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358 fout.write("%s\t%s\t%s\t%s\n" %(blk,key.strip(),mut,count))
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359 fout.flush()
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360
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361 #catch any remaining repeats, for instance if the orthologous position contained different repeat units
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362 for remaining_key in mut2.keys():
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363 mut = mut2[remaining_key][0]/mut2[remaining_key][1]
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364 mut = "%.2e" %(mut/num_generations)
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365 count = count2[remaining_key]
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366 if region == 'align':
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367 print >>fout, str(blk) + '\t'+seq1 + '\t'+seq2 + '\t'+remaining_key.strip()+ '\t'+str(mut)+ '\t'+ str(count)
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368 elif region == 'win':
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369 fout.write("%s\t%s\t%s\t%s\n" %(blk,remaining_key.strip(),mut,count))
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370 fout.flush()
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371 #print >>fout, blk + '\t'+remaining_key.strip()+ '\t'+str(mut)+ '\t'+ str(count)
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372
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373 def counter(node, start, end, report_func):
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374 if start <= node.start < end and start < node.end <= end:
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375 report_func(node)
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376 if node.right:
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377 counter(node.right, start, end, report_func)
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378 if node.left:
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379 counter(node.left, start, end, report_func)
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|
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380 elif node.start < start and node.right:
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381 counter(node.right, start, end, report_func)
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|
|
382 elif node.start >= end and node.left and node.left.maxend > start:
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|
|
383 counter(node.left, start, end, report_func)
|
|
|
384
|
|
|
385
|
|
|
386 def main():
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|
|
387 infile = sys.argv[1]
|
|
|
388
|
|
|
389 for i, line in enumerate( file ( infile )):
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|
|
390 line = line.rstrip('\r\n')
|
|
|
391 if len( line )>0 and not line.startswith( '#' ):
|
|
|
392 elems = line.split( '\t' )
|
|
|
393 break
|
|
|
394 if i == 30:
|
|
|
395 break # Hopefully we'll never get here...
|
|
|
396
|
|
|
397 if len( elems ) != 15:
|
|
|
398 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." )
|
|
|
399 global winspecies, speciesind
|
|
|
400 if region == 'win':
|
|
|
401 if dbkey_i in elems[1]:
|
|
|
402 winspecies = 1
|
|
|
403 speciesind = 1
|
|
|
404 elif dbkey_i in elems[8]:
|
|
|
405 winspecies = 2
|
|
|
406 speciesind = 8
|
|
|
407 else:
|
|
|
408 stop_err("The species build corresponding to your interval file is not present in the Microsatellite file.")
|
|
|
409
|
|
|
410 fin = open(infile, 'r')
|
|
|
411 skipped = 0
|
|
|
412 blk=0
|
|
|
413 win=0
|
|
|
414 linestr=""
|
|
|
415
|
|
|
416 if region == 'win':
|
|
|
417
|
|
|
418 msats = NiceReaderWrapper( fileinput.FileInput( infile ),
|
|
|
419 chrom_col = speciesind,
|
|
|
420 start_col = speciesind+1,
|
|
|
421 end_col = speciesind+2,
|
|
|
422 strand_col = -1,
|
|
|
423 fix_strand = True)
|
|
|
424 msatTree = quicksect.IntervalTree()
|
|
|
425 for item in msats:
|
|
|
426 if type( item ) is GenomicInterval:
|
|
|
427 msatTree.insert( item, msats.linenum, item.fields )
|
|
|
428
|
|
|
429 for iline in fint:
|
|
|
430 try:
|
|
|
431 iline = iline.rstrip('\r\n')
|
|
|
432 if not(iline) or iline == "":
|
|
|
433 continue
|
|
|
434 ielems = iline.strip("\r\n").split('\t')
|
|
|
435 ichr = ielems[chr_col_i]
|
|
|
436 istart = int(ielems[start_col_i])
|
|
|
437 iend = int(ielems[end_col_i])
|
|
|
438 isrc = "%s.%s" %(dbkey_i,ichr)
|
|
|
439 if isrc not in msatTree.chroms:
|
|
|
440 continue
|
|
|
441 result = []
|
|
|
442 root = msatTree.chroms[isrc] #root node for the chrom
|
|
|
443 counter(root, istart, iend, lambda node: result.append( node ))
|
|
|
444 if not(result):
|
|
|
445 continue
|
|
|
446 tmpfile1 = tempfile.NamedTemporaryFile('wb+')
|
|
|
447 for node in result:
|
|
|
448 tmpfile1.write("%s\n" % "\t".join( node.other ))
|
|
|
449
|
|
|
450 tmpfile1.seek(0)
|
|
|
451 output_writer(iline, tmpfile1.readlines())
|
|
|
452 except:
|
|
|
453 skipped+=1
|
|
|
454 if skipped:
|
|
|
455 print "Skipped %d intervals as invalid." %(skipped)
|
|
|
456 elif region == 'align':
|
|
|
457 if s_group_cols[0] != -1:
|
|
|
458 print >>fout, "#Window\tSpecies_1\tSpecies_2\tGroupby_Feature\tSubGroupby_Feature\tMutability\tCount"
|
|
|
459 else:
|
|
|
460 print >>fout, "#Window\tSpecies_1\tWindow_Start\tWindow_End\tSpecies_2\tGroupby_Feature\tMutability\tCount"
|
|
|
461 prev_bnum = -1
|
|
|
462 try:
|
|
|
463 for line in fin:
|
|
|
464 line = line.strip("\r\n")
|
|
|
465 if not(line) or line == "":
|
|
|
466 continue
|
|
|
467 elems = line.split('\t')
|
|
|
468 try:
|
|
|
469 assert int(elems[0])
|
|
|
470 assert len(elems) == 15
|
|
|
471 except:
|
|
|
472 continue
|
|
|
473 new_bnum = int(elems[0])
|
|
|
474 if new_bnum != prev_bnum:
|
|
|
475 if prev_bnum != -1:
|
|
|
476 output_writer(prev_bnum, linestr.strip().replace('\r','\n').split('\n'))
|
|
|
477 linestr = line + "\n"
|
|
|
478 else:
|
|
|
479 linestr += line
|
|
|
480 linestr += "\n"
|
|
|
481 prev_bnum = new_bnum
|
|
|
482 output_writer(prev_bnum, linestr.strip().replace('\r','\n').split('\n'))
|
|
|
483 except Exception, ea:
|
|
|
484 print >>sys.stderr, ea
|
|
|
485 skipped += 1
|
|
|
486 if skipped:
|
|
|
487 print "Skipped %d lines as invalid." %(skipped)
|
|
|
488 if __name__ == "__main__":
|
|
|
489 main() |
