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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
author mheinzl
date Thu, 10 May 2018 07:30:27 -0400
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239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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1 #!/usr/bin/env python
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2
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3 # Hamming distance analysis of SSCSs
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4 #
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5 # Author: Monika Heinzl, Johannes-Kepler University Linz (Austria)
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6 # Contact: monika.heinzl@edumail.at
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7 #
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8 # Takes at least one TABULAR file with tags before the alignment to the SSCS and optionally a second TABULAR file as input.
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9 # The program produces a plot which shows a histogram of Hamming distances separated after family sizes,
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10 # a family size distribution separated after Hamming distances for all (sample_size=0) or a given sample of SSCSs or SSCSs, which form a DCS.
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11 # In additon, the tool produces HD and FSD plots for the difference between the HDs of both parts of the tags and for the chimeric reads
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12 # and finally a CSV file with the data of the plots.
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13 # It is also possible to perform the HD analysis with shortened tags with given sizes as input.
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14 # The tool can run on a certain number of processors, which can be defined by the user.
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16 # USAGE: python HDnew6_1Plot_FINAL.py --inputFile filename --inputName1 filename --inputFile2 filename2 --inputName2 filename2 --sample_size int/0 --sep "characterWhichSeparatesCSVFile" /
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17 # --only_DCS True --FamilySize3 True --subset_tag True --nproc int --output_csv outptufile_name_csv --output_pdf outptufile_name_pdf
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18
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19 import numpy
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20 import itertools
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21 import operator
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22 import matplotlib.pyplot as plt
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23 import os.path
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24 import cPickle as pickle
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25 from multiprocessing.pool import Pool
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26 from functools import partial
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27 from HDAnalysis_plots.plot_HDwithFSD import plotHDwithFSD
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28 from HDAnalysis_plots.plot_FSDwithHD2 import plotFSDwithHD2
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29 from HDAnalysis_plots.plot_HDwithinSeq_Sum2 import plotHDwithinSeq_Sum2
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30 from HDAnalysis_plots.table_HD import createTableHD, createFileHD, createTableHDwithTags, createFileHDwithinTag
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31 from HDAnalysis_plots.table_FSD import createTableFSD2, createFileFSD2
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32 import argparse
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33 import sys
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34 import os
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35 from matplotlib.backends.backend_pdf import PdfPages
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36
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37 def hamming(array1, array2):
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38 res = 99 * numpy.ones(len(array1))
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39 i = 0
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40 array2 = numpy.unique(array2) # remove duplicate sequences to decrease running time
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41 for a in array1:
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42 dist = numpy.array([sum(itertools.imap(operator.ne, a, b)) for b in array2]) # fastest
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43 res[i] = numpy.amin(dist[dist > 0]) # pick min distance greater than zero
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44 #print(i)
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45 i += 1
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46 return res
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48 def hamming_difference(array1, array2, mate_b):
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49 array2 = numpy.unique(array2) # remove duplicate sequences to decrease running time
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50 array1_half = numpy.array([i[0:(len(i)) / 2] for i in array1]) # mate1 part1
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51 array1_half2 = numpy.array([i[len(i) / 2:len(i)] for i in array1]) # mate1 part 2
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52
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53 array2_half = numpy.array([i[0:(len(i)) / 2] for i in array2]) # mate2 part1
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54 array2_half2 = numpy.array([i[len(i) / 2:len(i)] for i in array2]) # mate2 part2
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55
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56 diff11 = []
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57 relativeDiffList = []
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58 ham1 = []
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59 ham2 = []
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60 min_valueList = []
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61 min_tagsList = []
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62 diff11_zeros = []
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63 min_tagsList_zeros = []
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64 i = 0 # counter, only used to see how many HDs of tags were already calculated
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65 if mate_b is False: # HD calculation for all a's
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66 half1_mate1 = array1_half
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67 half2_mate1 = array1_half2
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68 half1_mate2 = array2_half
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69 half2_mate2 = array2_half2
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70 elif mate_b is True: # HD calculation for all b's
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71 half1_mate1 = array1_half2
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72 half2_mate1 = array1_half
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73 half1_mate2 = array2_half2
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74 half2_mate2 = array2_half
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75
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76 for a, b, tag in zip(half1_mate1, half2_mate1, array1):
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77 ## exclude identical tag from array2, to prevent comparison to itself
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78 sameTag = numpy.where(array2 == tag)
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79 indexArray2 = numpy.arange(0, len(array2), 1)
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80 index_withoutSame = numpy.delete(indexArray2, sameTag) # delete identical tag from the data
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81
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82 # all tags without identical tag
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83 array2_half_withoutSame = half1_mate2[index_withoutSame]
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84 array2_half2_withoutSame = half2_mate2[index_withoutSame]
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85 #array2_withoutSame = array2[index_withoutSame] # whole tag (=not splitted into 2 halfs)
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86
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87 dist = numpy.array([sum(itertools.imap(operator.ne, a, c)) for c in
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88 array2_half_withoutSame]) # calculate HD of "a" in the tag to all "a's" or "b" in the tag to all "b's"
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89 min_index = numpy.where(dist == dist.min()) # get index of min HD
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90 min_value = dist[min_index] # get minimum HDs
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91 min_tag_half2 = array2_half2_withoutSame[min_index] # get all "b's" of the tag or all "a's" of the tag with minimum HD
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92 #min_tag = array2_withoutSame[min_index] # get whole tag with min HD
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93
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94 dist2 = numpy.array([sum(itertools.imap(operator.ne, b, e)) for e in
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95 min_tag_half2]) # calculate HD of "b" to all "b's" or "a" to all "a's"
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96 for d_1, d_2 in zip(min_value, dist2):
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97 if mate_b is True: # half2, corrects the variable of the HD from both halfs if it is a or b
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98 d = d_2
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99 d2 = d_1
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100 else: # half1, corrects the variable of the HD from both halfs if it is a or b
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101 d = d_1
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102 d2 = d_2
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103 min_valueList.append(d + d2)
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104 min_tagsList.append(tag)
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105 ham1.append(d)
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106 ham2.append(d2)
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107 difference1 = abs(d - d2)
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108 diff11.append(difference1)
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109 rel_difference = round(float(difference1) / (d + d2), 1)
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110 relativeDiffList.append(rel_difference)
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111
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112 #### tags which have identical parts:
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113 if d == 0 or d2 == 0:
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114 min_tagsList_zeros.append(tag)
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115 difference1_zeros = abs(d - d2)
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116 diff11_zeros.append(difference1_zeros)
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117 #print(i)
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118 i += 1
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119 return ([diff11, ham1, ham2, min_valueList, min_tagsList, relativeDiffList, diff11_zeros, min_tagsList_zeros])
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120
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121 def readFileReferenceFree(file):
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122 with open(file, 'r') as dest_f:
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123 data_array = numpy.genfromtxt(dest_f, skip_header=0, delimiter='\t', comments='#', dtype='string')
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124 integers = numpy.array(data_array[:, 0]).astype(int)
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125 return(integers, data_array)
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126
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127 def hammingDistanceWithFS(quant, ham):
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128 quant = numpy.asarray(quant)
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129 maximum = max(ham)
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130 minimum = min(ham)
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131 ham = numpy.asarray(ham)
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132
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133 singletons = numpy.where(quant == 1)[0]
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134 data = ham[singletons]
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135
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136 hd2 = numpy.where(quant == 2)[0]
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137 data2 = ham[hd2]
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138
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139 hd3 = numpy.where(quant == 3)[0]
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140 data3 = ham[hd3]
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141
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142 hd4 = numpy.where(quant == 4)[0]
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143 data4 = ham[hd4]
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144
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145 hd5 = numpy.where((quant >= 5) & (quant <= 10))[0]
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146 data5 = ham[hd5]
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147
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148 hd6 = numpy.where(quant > 10)[0]
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149 data6 = ham[hd6]
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150
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151 list1 = [data, data2, data3, data4, data5, data6]
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152 return(list1, maximum, minimum)
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153
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154 def familySizeDistributionWithHD(fs, ham, diff=False, rel = True):
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155 hammingDistances = numpy.unique(ham)
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156 fs = numpy.asarray(fs)
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157
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158 ham = numpy.asarray(ham)
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159 bigFamilies2 = numpy.where(fs > 19)[0]
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160 if len(bigFamilies2) != 0:
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161 fs[bigFamilies2] = 20
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162 maximum = max(fs)
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163 minimum = min(fs)
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164 if diff is True:
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165 hd0 = numpy.where(ham == 0)[0]
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166 data0 = fs[hd0]
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167
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168 if rel is True:
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169 hd1 = numpy.where(ham == 0.1)[0]
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170 else:
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171 hd1 = numpy.where(ham == 1)[0]
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172 data = fs[hd1]
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173
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174 if rel is True:
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175 hd2 = numpy.where(ham == 0.2)[0]
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176 else:
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177 hd2 = numpy.where(ham == 2)[0]
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178 data2 = fs[hd2]
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179
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180 if rel is True:
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181 hd3 = numpy.where(ham == 0.3)[0]
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182 else:
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183 hd3 = numpy.where(ham == 3)[0]
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184 data3 = fs[hd3]
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185
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186 if rel is True:
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187 hd4 = numpy.where(ham == 0.4)[0]
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188 else:
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189 hd4 = numpy.where(ham == 4)[0]
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190 data4 = fs[hd4]
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191
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192 if rel is True:
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193 hd5 = numpy.where((ham >= 0.5) & (ham <= 0.8))[0]
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194 else:
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195 hd5 = numpy.where((ham >= 5) & (ham <= 8))[0]
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196 data5 = fs[hd5]
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197
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198 if rel is True:
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199 hd6 = numpy.where(ham > 0.8)[0]
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200 else:
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201 hd6 = numpy.where(ham > 8)[0]
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202 data6 = fs[hd6]
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203
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204 if diff is True:
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205 list1 = [data0,data, data2, data3, data4, data5, data6]
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206 else:
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207 list1 = [data, data2, data3, data4, data5, data6]
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208
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209 return(list1, hammingDistances, maximum, minimum)
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210
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211 def make_argparser():
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212 parser = argparse.ArgumentParser(description='Hamming distance analysis of duplex sequencing data')
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213 parser.add_argument('--inputFile',
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214 help='Tabular File with three columns: ab or ba, tag and family size.')
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215 parser.add_argument('--inputName1')
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216 parser.add_argument('--inputFile2',default=None,
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217 help='Tabular File with three columns: ab or ba, tag and family size.')
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218 parser.add_argument('--inputName2')
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219 parser.add_argument('--sample_size', default=1000,type=int,
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220 help='Sample size of Hamming distance analysis.')
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221 parser.add_argument('--sep', default=",",
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222 help='Separator in the csv file.')
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223 parser.add_argument('--subset_tag', default=0,type=int,
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224 help='The tag is shortened to the given number.')
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225 parser.add_argument('--nproc', default=4,type=int,
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226 help='The tool runs with the given number of processors.')
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227 parser.add_argument('--only_DCS', action="store_false", # default=False, type=bool,
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228 help='Only tags of the DCSs are included in the HD analysis')
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229
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230 parser.add_argument('--minFS', default=1, type=int,
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231 help='Only tags, which have a family size greater or equal than specified, are included in the HD analysis')
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232 parser.add_argument('--maxFS', default=0, type=int,
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233 help='Only tags, which have a family size smaller or equal than specified, are included in the HD analysis')
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234
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235 parser.add_argument('--output_csv', default="data.csv", type=str,
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236 help='Name of the csv file.')
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237 parser.add_argument('--output_pdf', default="data.pdf", type=str,
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238 help='Name of the pdf file.')
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239 parser.add_argument('--output_pdf2', default="data2.pdf", type=str,
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240 help='Name of the pdf file.')
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241 parser.add_argument('--output_csv2', default="data2.csv", type=str,
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242 help='Name of the csv file.')
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243
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244 return parser
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245
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246 def Hamming_Distance_Analysis(argv):
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247 parser = make_argparser()
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248 args = parser.parse_args(argv[1:])
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249
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250 file1 = args.inputFile
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251 name1 = args.inputName1
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252
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253 file2 = args.inputFile2
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254 name2 = args.inputName2
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255
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256 index_size = args.sample_size
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257 title_savedFile_pdf = args.output_pdf
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258 title_savedFile_pdf2 = args.output_pdf2
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259
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260 title_savedFile_csv = args.output_csv
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261 title_savedFile_csv2 = args.output_csv2
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262
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263 sep = args.sep
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264 onlyDuplicates = args.only_DCS
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265 minFS = args.minFS
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266 maxFS = args.maxFS
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267
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268 subset = args.subset_tag
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269 nproc = args.nproc
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270
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271 ### input checks
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272 if index_size < 0:
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273 print("index_size is a negative integer.")
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274 exit(2)
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275
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276 if nproc <= 0:
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277 print("nproc is smaller or equal zero")
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278 exit(3)
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279
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280 if type(sep) is not str or len(sep)>1:
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281 print("sep must be a single character.")
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282 exit(4)
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283
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284 if subset < 0:
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285 print("subset_tag is smaller or equal zero.")
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286 exit(5)
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287
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288 ### PLOT ###
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289 plt.rcParams['axes.facecolor'] = "E0E0E0" # grey background color
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290 plt.rcParams['xtick.labelsize'] = 12
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291 plt.rcParams['ytick.labelsize'] = 12
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292 plt.rcParams['patch.edgecolor'] = "#000000"
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293 plt.rc('figure', figsize=(11.69, 8.27)) # A4 format
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294
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295 if file2 != str(None):
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296 files = [file1, file2]
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297 name1 = name1.split(".tabular")[0]
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298 name2 = name2.split(".tabular")[0]
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299 names = [name1, name2]
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300 pdf_files = [title_savedFile_pdf, title_savedFile_pdf2]
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301 csv_files = [title_savedFile_csv, title_savedFile_csv2]
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302 else:
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303 files = [file1]
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304 name1 = name1.split(".tabular")[0]
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305 names = [name1]
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306 pdf_files = [title_savedFile_pdf]
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307 csv_files = [title_savedFile_csv]
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308
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309 print(type(onlyDuplicates))
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310 print(onlyDuplicates)
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311
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312 for f, name_file, pdf_f, csv_f in zip(files, names, pdf_files, csv_files):
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313 with open(csv_f, "w") as output_file, PdfPages(pdf_f) as pdf:
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314 print("dataset: ", name_file)
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315 integers, data_array = readFileReferenceFree(f)
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316 data_array = numpy.array(data_array)
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317 int_f = numpy.array(data_array[:, 0]).astype(int)
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318 data_array = data_array[numpy.where(int_f >= minFS)]
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319 integers = integers[integers >= minFS]
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320
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321 # select family size for tags
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322 if maxFS > 0:
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323 int_f2 = numpy.array(data_array[:, 0]).astype(int)
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324 data_array = data_array[numpy.where(int_f2 <= maxFS)]
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325 integers = integers[integers <= maxFS]
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326
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327 print("min FS", min(integers))
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328 print("max FS", max(integers))
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329
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330 tags = data_array[:, 2]
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331 seq = data_array[:, 1]
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332
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333 if onlyDuplicates is True:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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334 # find all unique tags and get the indices for ALL tags, but only once
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335 u, index_unique, c = numpy.unique(numpy.array(seq), return_counts=True, return_index=True)
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336 d = u[c > 1]
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337
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338 # get family sizes, tag for duplicates
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339 duplTags_double = integers[numpy.in1d(seq, d)]
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340 duplTags = duplTags_double[0::2] # ab of DCS
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341 duplTagsBA = duplTags_double[1::2] # ba of DCS
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342
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343 duplTags_tag = tags[numpy.in1d(seq, d)][0::2] # ab
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344 duplTags_seq = seq[numpy.in1d(seq, d)][0::2] # ab - tags
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345
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346 data_array = numpy.column_stack((duplTags, duplTags_seq))
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347 data_array = numpy.column_stack((data_array, duplTags_tag))
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348 integers = numpy.array(data_array[:, 0]).astype(int)
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349 print("DCS in whole dataset", len(data_array))
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350
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351 ## HD analysis for a subset of the tag
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352 if subset > 0:
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353 tag1 = numpy.array([i[0:(len(i)) / 2] for i in data_array[:, 1]])
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354 tag2 = numpy.array([i[len(i) / 2:len(i)] for i in data_array[:, 1]])
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355
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356 flanking_region_float = float((len(tag1[0]) - subset)) / 2
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357 flanking_region = int(flanking_region_float)
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358 if flanking_region_float % 2 == 0:
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359 tag1_shorten = numpy.array([i[flanking_region:len(i) - flanking_region] for i in tag1])
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diff changeset
360 tag2_shorten = numpy.array([i[flanking_region:len(i) - flanking_region] for i in tag2])
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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parents:
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361 else:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
362 flanking_region_rounded = int(round(flanking_region, 1))
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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363 flanking_region_rounded_end = len(tag1[0]) - subset - flanking_region_rounded
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
364 tag1_shorten = numpy.array(
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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365 [i[flanking_region:len(i) - flanking_region_rounded_end] for i in tag1])
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
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366 tag2_shorten = numpy.array(
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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367 [i[flanking_region:len(i) - flanking_region_rounded_end] for i in tag2])
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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368
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mheinzl
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369 data_array_tag = numpy.array([i + j for i, j in zip(tag1_shorten, tag2_shorten)])
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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370 data_array = numpy.column_stack((data_array[:, 0], data_array_tag, data_array[:, 2]))
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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371
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372 print("length of tag= ", len(data_array[0, 1]))
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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373 # select sample: if no size given --> all vs. all comparison
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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374 if index_size == 0:
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375 result = numpy.arange(0, len(data_array), 1)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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376 else:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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377 result = numpy.random.choice(len(integers), size=index_size,
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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378 replace=False) # array of random sequences of size=index.size
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379
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380 # with open("index_result1_{}.pkl".format(app_f), "wb") as o:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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381 # pickle.dump(result, o, pickle.HIGHEST_PROTOCOL)
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382
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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383 # comparison random tags to whole dataset
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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384 result1 = data_array[result, 1] # random tags
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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385 result2 = data_array[:, 1] # all tags
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386 print("size of the whole dataset= ", len(result2))
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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387 print("sample size= ", len(result1))
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mheinzl
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388
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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389 # HD analysis of whole tag
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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390 proc_pool = Pool(nproc)
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391 chunks_sample = numpy.array_split(result1, nproc)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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392 ham = proc_pool.map(partial(hamming, array2=result2), chunks_sample)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
393 proc_pool.close()
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
394 proc_pool.join()
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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diff changeset
395 ham = numpy.concatenate(ham).astype(int)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
396 # with open("HD_whole dataset_{}.txt".format(app_f), "w") as output_file1:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
397 # for h, tag in zip(ham, result1):
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
398 # output_file1.write("{}\t{}\n".format(tag, h))
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
399
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
400 # HD analysis for chimeric reads
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
401 proc_pool_b = Pool(nproc)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
402 diff_list_a = proc_pool_b.map(partial(hamming_difference, array2=result2, mate_b=False), chunks_sample)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
403 diff_list_b = proc_pool_b.map(partial(hamming_difference, array2=result2, mate_b=True), chunks_sample)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
404 proc_pool_b.close()
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
405 proc_pool_b.join()
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
406 diff = numpy.concatenate((numpy.concatenate([item[0] for item in diff_list_a]),
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
407 numpy.concatenate([item_b[0] for item_b in diff_list_b]))).astype(int)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
408 HDhalf1 = numpy.concatenate((numpy.concatenate([item[1] for item in diff_list_a]),
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
409 numpy.concatenate([item_b[1] for item_b in diff_list_b]))).astype(int)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
410 HDhalf2 = numpy.concatenate((numpy.concatenate([item[2] for item in diff_list_a]),
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
411 numpy.concatenate([item_b[2] for item_b in diff_list_b]))).astype(int)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
412 minHDs = numpy.concatenate((numpy.concatenate([item[3] for item in diff_list_a]),
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
413 numpy.concatenate([item_b[3] for item_b in diff_list_b]))).astype(int)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
414 minHD_tags = numpy.concatenate((numpy.concatenate([item[4] for item in diff_list_a]),
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
415 numpy.concatenate([item_b[4] for item_b in diff_list_b])))
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
416 rel_Diff = numpy.concatenate((numpy.concatenate([item[5] for item in diff_list_a]),
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
417 numpy.concatenate([item_b[5] for item_b in diff_list_b])))
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
418 diff_zeros = numpy.concatenate((numpy.concatenate([item[6] for item in diff_list_a]),
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
419 numpy.concatenate([item_b[6] for item_b in diff_list_b]))).astype(int)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
420 minHD_tags_zeros = numpy.concatenate((numpy.concatenate([item[7] for item in diff_list_a]),
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
421 numpy.concatenate([item_b[7] for item_b in diff_list_b])))
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
422
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
423 # with open("HD_within tag_{}.txt".format(app_f), "w") as output_file2:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
424 # for d, s1, s2, hd, rel_d, tag in zip(diff, HDhalf1, HDhalf2, minHDs, rel_Diff, minHD_tags):
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
425 # output_file2.write(
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
426 # "{}\t{}\t{}\t{}\t{}\t{}\n".format(tag, hd, s1, s2, d, rel_d))
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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parents:
diff changeset
427
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mheinzl
parents:
diff changeset
428 lenTags = len(data_array)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
429
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parents:
diff changeset
430 quant = numpy.array(data_array[result, 0]).astype(int) # family size for sample of tags
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
431 seq = numpy.array(data_array[result, 1]) # tags of sample
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
432 ham = numpy.asarray(ham) # HD for sample of tags
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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parents:
diff changeset
433
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parents:
diff changeset
434 if onlyDuplicates is True: # ab and ba strands of DCSs
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
435 quant = numpy.concatenate((quant, duplTagsBA[result]))
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
436 seq = numpy.tile(seq, 2)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
437 ham = numpy.tile(ham, 2)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
438
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
439 # prepare data for different kinds of plots
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
440 list1, maximumX, minimumX = hammingDistanceWithFS(quant, ham) # histogram of HDs separated after FS
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
441 # distribution of FSs separated after HD
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
442 familySizeList1, hammingDistances, maximumXFS, minimumXFS = familySizeDistributionWithHD(quant, ham,
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
443 rel=False)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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parents:
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444
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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diff changeset
445 ## get FS for all tags with min HD of analysis of chimeric reads
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
446 # there are more tags than sample size in the plot, because one tag can have multiple minimas
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
447 seqDic = dict(zip(seq, quant))
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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448 lst_minHD_tags = []
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
449 for i in minHD_tags:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
450 lst_minHD_tags.append(seqDic.get(i))
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
451
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
452 # histogram with absolute and relative difference between HDs of both parts of the tag
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
453 listDifference1, maximumXDifference, minimumXDifference = hammingDistanceWithFS(lst_minHD_tags, diff)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
454 listRelDifference1, maximumXRelDifference, minimumXRelDifference = hammingDistanceWithFS(lst_minHD_tags,
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
455 rel_Diff)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
456
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
457 # family size distribution separated after the difference between HDs of both parts of the tag
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
458 familySizeList1_diff, hammingDistances_diff, maximumXFS_diff, minimumXFS_diff = familySizeDistributionWithHD(
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
459 lst_minHD_tags, diff, diff=True, rel=False)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
460 familySizeList1_reldiff, hammingDistances_reldiff, maximumXFS_reldiff, minimumXFS_reldiff = familySizeDistributionWithHD(
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
461 lst_minHD_tags, rel_Diff, diff=True, rel=True)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
462
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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463 # chimeric read analysis: tags which have HD=0 in one of the halfs
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
464 if len(minHD_tags_zeros) != 0:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
465 lst_minHD_tags_zeros = []
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
466 for i in minHD_tags_zeros:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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467 lst_minHD_tags_zeros.append(seqDic.get(i)) # get family size for tags of chimeric reads
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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468
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
469 # histogram with HD of non-identical half
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
470 listDifference1_zeros, maximumXDifference_zeros, minimumXDifference_zeros = hammingDistanceWithFS(
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
471 lst_minHD_tags_zeros, diff_zeros)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
472 # family size distribution of non-identical half
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
473 familySizeList1_diff_zeros, hammingDistances_diff_zeros, maximumXFS_diff_zeros, minimumXFS_diff_zeros = familySizeDistributionWithHD(
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
474 lst_minHD_tags_zeros, diff_zeros, diff=False, rel=False)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
475
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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476 ########################## Plot HD within tags ########################################################
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
477 ######################################################################################################################
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
478 plotHDwithinSeq_Sum2(HDhalf1, HDhalf2, minHDs, pdf=pdf, lenTags=lenTags, title_file1=name_file)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
479
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
480 #####################################################################################################################
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
481 ################## plot Hamming Distance with Family size distribution ##############################
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
482 #####################################################################################################################
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
483 plotHDwithFSD(list1=list1, maximumX=maximumX, minimumX=minimumX, pdf=pdf,
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
484 subtitle="Overall hamming distance with separation after family size", title_file1=name_file,
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
485 lenTags=lenTags,xlabel="Hamming distance")
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
486
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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487 ########################## Plot FSD with separation after HD ###############################################
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
488 ########################################################################################################################
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
489 plotFSDwithHD2(familySizeList1, maximumXFS, minimumXFS,
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
490 quant=quant, subtitle="Family size distribution with separation after hamming distance",
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
491 pdf=pdf,relative=False, title_file1=name_file, diff=False)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
492
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
493 ########################## Plot difference between HD's separated after FSD ##########################################
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
494 ########################################################################################################################
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
495 plotHDwithFSD(listDifference1, maximumXDifference, minimumXDifference, pdf=pdf,
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
496 subtitle="Delta Hamming distances within tags with separation after family size",
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
497 title_file1=name_file, lenTags=lenTags,
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
498 xlabel="absolute delta Hamming distance", relative=False)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
499
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
500 plotHDwithFSD(listRelDifference1, maximumXRelDifference, minimumXRelDifference, pdf=pdf,
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
501 subtitle="Relative delta Hamming distances within tags with separation after family size",
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
502 title_file1=name_file, lenTags=lenTags,
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
503 xlabel="relative delta Hamming distance", relative=True)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
504
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
505 #################### Plot FSD separated after difference between HD's #####################################
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
506 ########################################################################################################################
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
507 plotFSDwithHD2(familySizeList1_diff, maximumXFS_diff, minimumXFS_diff,
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
508 subtitle="Family size distribution with separation after delta Hamming distances within the tags",
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
509 pdf=pdf,relative=False, diff=True, title_file1=name_file, quant=quant)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
510
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
511 plotFSDwithHD2(familySizeList1_reldiff, maximumXFS_reldiff, minimumXFS_reldiff, quant=quant, pdf=pdf,
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
512 subtitle="Family size distribution with separation after delta Hamming distances within the tags",
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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513 relative=True, diff=True, title_file1=name_file)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
514
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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parents:
diff changeset
515
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
516 # plots for chimeric reads
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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517 if len(minHD_tags_zeros) != 0:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
518 ## HD
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
519 plotHDwithFSD(listDifference1_zeros, maximumXDifference_zeros, minimumXDifference_zeros, pdf=pdf,
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
520 subtitle="Hamming Distance of the non-identical half with separation after family size"
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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521 "\n(at least one half is identical with the half of the min. tag)\n",
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
522 title_file1=name_file, lenTags=lenTags,xlabel="Hamming distance", relative=False)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
523
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
524 ## FSD
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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525 plotFSDwithHD2(familySizeList1_diff_zeros, maximumXFS_diff_zeros, minimumXFS_diff_zeros,
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
526 quant=quant, pdf=pdf,
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
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527 subtitle="Family size distribution with separation after hamming distances from the non-identical half\n"
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
528 "(at least one half is identical with the half of the min. tag)\n",
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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529 relative=False, diff=False, title_file1=name_file)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
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530
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
531 ### print all data to a CSV file
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
532 #### HD ####
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
533 summary, sumCol = createTableHD(list1, "HD=")
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
534 overallSum = sum(sumCol) # sum of columns in table
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
535
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
536 #### FSD ####
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
537 summary5, sumCol5 = createTableFSD2(familySizeList1, diff=False)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
538 overallSum5 = sum(sumCol5)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
539
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
540 ### HD of both parts of the tag ####
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
541 summary9, sumCol9 = createTableHDwithTags([numpy.array(minHDs), HDhalf1, HDhalf2])
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
542 overallSum9 = sum(sumCol9)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
543
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
544 ## HD
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
545 # absolute difference
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
546 summary11, sumCol11 = createTableHD(listDifference1, "diff=")
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
547 overallSum11 = sum(sumCol11)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
548 # relative difference and all tags
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
549 summary13, sumCol13 = createTableHD(listRelDifference1, "diff=")
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
550 overallSum13 = sum(sumCol13)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
551
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
552 ## FSD
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
553 # absolute difference
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
554 summary19, sumCol19 = createTableFSD2(familySizeList1_diff)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
555 overallSum19 = sum(sumCol19)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
556 # relative difference
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
557 summary21, sumCol21 = createTableFSD2(familySizeList1_reldiff)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
558 overallSum21 = sum(sumCol21)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
559
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
560 # chimeric reads
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
561 if len(minHD_tags_zeros) != 0:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
562 # absolute difference and tags where at least one half has HD=0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
563 summary15, sumCol15 = createTableHD(listDifference1_zeros, "diff=")
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
564 overallSum15 = sum(sumCol15)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
565 # absolute difference and tags where at least one half has HD=0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
566 summary23, sumCol23 = createTableFSD2(familySizeList1_diff_zeros, diff=False)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
567 overallSum23 = sum(sumCol23)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
568
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
569 output_file.write("{}\n".format(f))
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
570 output_file.write("number of tags per file{}{:,} (from {:,}) against {:,}\n\n".format(sep, len(
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
571 numpy.concatenate(list1)), lenTags, lenTags))
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
572
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
573 ### HD ###
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
574 createFileHD(summary, sumCol, overallSum, output_file,
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
575 "Hamming distance with separation after family size: file1", sep)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
576 ### FSD ###
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
577 createFileFSD2(summary5, sumCol5, overallSum5, output_file,
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
578 "Family size distribution with separation after hamming distances: file1", sep,
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
579 diff=False)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
580
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
581 count = numpy.bincount(quant)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
582 output_file.write("{}{}\n".format(sep, f))
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
583 output_file.write("max. family size:{}{}\n".format(sep, max(quant)))
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
584 output_file.write("absolute frequency:{}{}\n".format(sep, count[len(count) - 1]))
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
585 output_file.write(
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
586 "relative frequency:{}{}\n\n".format(sep, float(count[len(count) - 1]) / sum(count)))
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
587
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
588 ### HD within tags ###
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
589 output_file.write(
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
590 "The hamming distances were calculated by comparing each half of all tags against the tag(s) with the minimum Hamming distance per half.\n"
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
591 "It is possible that one tag can have the minimum HD from multiple tags, so the sample size in this calculation differs from the sample size entered by the user.\n")
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
592 output_file.write(
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
593 "file 1: actual number of tags with min HD = {:,} (sample size by user = {:,})\n".format(
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
594 len(numpy.concatenate(listDifference1)), len(numpy.concatenate(list1))))
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
595 output_file.write("length of one part of the tag = {}\n\n".format(len(data_array[0, 1]) / 2))
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
596
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
597 createFileHDwithinTag(summary9, sumCol9, overallSum9, output_file,
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
598 "Hamming distance of each half in the tag: file1", sep)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
599 createFileHD(summary11, sumCol11, overallSum11, output_file,
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
600 "Absolute delta Hamming distances within the tag: file1", sep)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
601 createFileHD(summary13, sumCol13, overallSum13, output_file,
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
602 "Relative delta Hamming distances within the tag: file1", sep)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
603
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
604 createFileFSD2(summary19, sumCol19, overallSum19, output_file,
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
605 "Family size distribution with separation after absolute delta Hamming distances: file1",
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
606 sep)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
607 createFileFSD2(summary21, sumCol21, overallSum21, output_file,
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
608 "Family size distribution with separation after relative delta Hamming distances: file1",
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
609 sep, rel=True)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
610
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
611 if len(minHD_tags_zeros) != 0:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
612 output_file.write(
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
613 "All tags were filtered: only those tags where at least one half is identical with the half of the min. tag are kept.\nSo the hamming distance of the non-identical half is compared.\n")
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
614 createFileHD(summary15, sumCol15, overallSum15, output_file,
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
615 "Hamming distances of non-zero half: file1", sep)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
616 createFileFSD2(summary23, sumCol23, overallSum23, output_file,
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
617 "Family size distribution with separation after Hamming distances of non-zero half: file1",
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
618 sep, diff=False)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
619 output_file.write("\n")
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
620
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
621
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
622
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
623 if __name__ == '__main__':
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
624 sys.exit(Hamming_Distance_Analysis(sys.argv))