annotate hd.py @ 16:ea67840d0514 draft

planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 797ff8e0461392fe4542de33e7b58f9e0abefc7c
author mheinzl
date Wed, 23 May 2018 14:31:48 -0400
parents cf7874bb4934
children 4a30328b1af9
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239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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1 #!/usr/bin/env python
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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 --minFS int --maxFS int --nr_above_bars True/False--output_csv outptufile_name_csv --output_pdf outptufile_name_pdf
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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 import argparse
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28 import sys
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29 import os
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30 from matplotlib.backends.backend_pdf import PdfPages
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31 from collections import Counter
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33 def plotFSDwithHD2(familySizeList1,maximumXFS,minimumXFS, originalCounts,
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34 title_file1, subtitle, pdf, relative=False, diff = True):
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35 if diff is False:
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36 colors = ["#e6194b", "#3cb44b", "#ffe119", "#0082c8", "#f58231", "#911eb4"]
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37 labels = ["HD=1", "HD=2", "HD=3", "HD=4", "HD=5-8","HD>8"]
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38 else:
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39 colors = ["#93A6AB", "#403C14", "#731E41", "#BAB591", "#085B6F", "#E8AA35", "#726C66"]
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40 if relative is True:
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41 labels = ["d=0", "d=0.1", "d=0.2", "d=0.3", "d=0.4", "d=0.5-0.8", "d>0.8"]
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42 else:
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43 labels = ["d=0","d=1", "d=2", "d=3", "d=4", "d=5-8","d>8"]
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44
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45 fig = plt.figure(figsize=(6, 7))
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46 ax = fig.add_subplot(111)
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47 plt.subplots_adjust(bottom=0.1)
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48 p1 = numpy.bincount(numpy.concatenate((familySizeList1)))
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49 maximumY = numpy.amax(p1)
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50
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51 if len(range(minimumXFS, maximumXFS)) == 0:
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52 range1 = range(minimumXFS - 1, minimumXFS + 2)
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53 else:
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54 range1 = range(0, maximumXFS + 2)
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55 counts = plt.hist(familySizeList1, label=labels,
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56 color=colors, stacked=True,
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57 rwidth=0.8,alpha=1, align="left",
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58 edgecolor="None",bins=range1)
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59 plt.legend(loc='upper right', fontsize=14, frameon=True, bbox_to_anchor=(1.45, 1))
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60
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61 #plt.title(title_file1, fontsize=12)
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62 plt.suptitle(subtitle, y=1, x=0.5, fontsize=14)
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63 plt.xlabel("Family size", fontsize=14)
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64 plt.ylabel("Absolute Frequency", fontsize=14)
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65
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66 ticks = numpy.arange(0, maximumXFS + 1, 1)
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67 ticks1 = map(str, ticks)
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68 if maximumXFS >= 20:
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69 ticks1[len(ticks1) - 1] = ">=20"
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70 plt.xticks(numpy.array(ticks), ticks1)
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71 [l.set_visible(False) for (i, l) in enumerate(ax.get_xticklabels()) if i % 5 != 0]
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72
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73 plt.xlim((0, maximumXFS + 1))
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74 if len(numpy.concatenate(familySizeList1)) != 0:
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75 plt.ylim((0, max(numpy.bincount(numpy.concatenate(familySizeList1))) * 1.1))
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76
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77 plt.ylim((0, maximumY * 1.2))
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78 legend = "\nmax. family size: \nabsolute frequency: \nrelative frequency: "
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79 plt.text(0.15, -0.08, legend, size=12, transform=plt.gcf().transFigure)
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80
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81 count = numpy.bincount(originalCounts) # original counts
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82 legend1 = "{}\n{}\n{:.5f}" \
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83 .format(max(originalCounts), count[len(count) - 1], float(count[len(count) - 1]) / sum(count))
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84 plt.text(0.5, -0.08, legend1, size=12, transform=plt.gcf().transFigure)
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85 legend3 = "singletons\n{:,}\n{:.5f}".format(int(counts[0][len(counts[0]) - 1][1]),
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86 float(counts[0][len(counts[0]) - 1][1]) / sum(
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87 counts[0][len(counts[0]) - 1]))
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88 plt.text(0.7, -0.08, legend3, transform=plt.gcf().transFigure, size=12)
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89 plt.grid(b=True, which='major', color='#424242', linestyle=':')
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90
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91 pdf.savefig(fig, bbox_inches="tight")
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92 plt.close("all")
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93
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94 def plotHDwithFSD(list1,maximumX,minimumX, subtitle, lenTags, title_file1,pdf,
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95 xlabel,relative=False, nr_above_bars = True):
1
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96 if relative is True:
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97 step = 0.1
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98 else:
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99 step = 1
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100
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101 fig = plt.figure(figsize=(6, 8))
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102 plt.subplots_adjust(bottom=0.1)
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103 con_list1 = numpy.concatenate(list1)
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104 p1 = numpy.array([v for k, v in sorted(Counter(con_list1).iteritems())])
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105 maximumY = numpy.amax(p1)
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106
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107 if relative is True: # relative difference
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108 bin1 = numpy.arange(-1, maximumX + 0.2, 0.1)
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109 else:
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110 bin1 = maximumX + 1
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111
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112 counts = plt.hist(list1, bins=bin1, edgecolor='black', linewidth=1,
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113 label=["FS=1", "FS=2", "FS=3", "FS=4", "FS=5-10",
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114 "FS>10"], rwidth=0.8,
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115 color=["#808080", "#FFFFCC", "#FFBF00", "#DF0101", "#0431B4", "#86B404"],
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116 stacked=True, alpha=1,
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117 align="left",
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118 range=(0, maximumX + 1))
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119 plt.legend(loc='upper right', fontsize=14, frameon=True, bbox_to_anchor=(1.45, 1))
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120 bins = counts[1] # width of bins
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121 counts = numpy.array(map(int, counts[0][5]))
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122 plt.suptitle(subtitle, y=1, x=0.5, fontsize=14)
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123 # plt.title(title_file1, fontsize=12)
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124 plt.xlabel(xlabel, fontsize=14)
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125 plt.ylabel("Absolute Frequency", fontsize=14)
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126
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127 plt.grid(b=True, which='major', color='#424242', linestyle=':')
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128 plt.axis((minimumX - step, maximumX + step, 0, numpy.amax(counts) + sum(counts) * 0.1))
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129 plt.xticks(numpy.arange(0, maximumX + step, step))
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130
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131 plt.ylim((0, maximumY * 1.2))
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132
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133 if nr_above_bars is True:
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134 bin_centers = -0.4 * numpy.diff(bins) + bins[:-1]
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135 for x_label, label in zip(counts, bin_centers): # labels for values
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136 if x_label == 0:
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137 continue
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138 else:
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139 plt.annotate("{:,}\n{:.3f}".format(x_label, float(x_label) / sum(counts), 1),
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140 xy=(label, x_label + len(con_list1) * 0.01),
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141 xycoords="data", color="#000066",fontsize=10)
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142
1
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143 legend = "sample size= {:,} against {:,}".format(sum(counts), lenTags)
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144 plt.text(0.14, -0.01, legend, size=12, transform=plt.gcf().transFigure)
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145
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146 pdf.savefig(fig, bbox_inches="tight")
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147 plt.close("all")
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148 plt.clf()
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149
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150 def plotHDwithinSeq_Sum2(sum1, sum2,sum1min, sum2min, min_value, lenTags, title_file1, pdf):
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151 fig = plt.figure(figsize=(6, 8))
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152 plt.subplots_adjust(bottom=0.1)
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153
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154 #ham = [sum1, sum2,numpy.array(min_value)] # new hd within tags
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155 ham = [sum1, sum2, sum1min, sum2min, numpy.array(min_value)] # new hd within tags
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156
1
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157
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158 maximumX = numpy.amax(numpy.concatenate(ham))
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159 minimumX = numpy.amin(numpy.concatenate(ham))
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160 maximumY = numpy.amax(numpy.concatenate(map(lambda (x): numpy.bincount(x), ham)))
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161
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162 if len(range(minimumX, maximumX)) == 0:
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163 range1 = minimumX
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164 else:
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165 range1 = range(minimumX, maximumX + 2)
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166
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167 counts = plt.hist(ham, align="left", rwidth=0.8, stacked=False,
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168 # label=[ "HD a", "HD b","HD a+b"],
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169 label=[ "HD a","HD b'", "HD b", "HD a'", "HD a+b"],
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170 #bins=range1, color=[ "#58ACFA", "#FA5858","#585858"],
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171 color=["#58ACFA", "#0404B4", "#FE642E", "#B40431", "#585858"],
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172 edgecolor='black', linewidth=1)
1
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173 plt.legend(loc='upper right', fontsize=14, frameon=True, bbox_to_anchor=(1.55, 1))
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174 plt.suptitle('Hamming distances within tags', fontsize=14)
2
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175 #plt.title(title_file1, fontsize=12)
14
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176 plt.xlabel("HD", fontsize=14)
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177 plt.ylabel("Absolute Frequency", fontsize=14)
1
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178 plt.grid(b=True, which='major', color='#424242', linestyle=':')
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179
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180
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181 plt.axis((minimumX - 1, maximumX + 1, 0, maximumY * 1.1))
2
316fbf91dd12 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit f9d5547849dabb59a33a5e998bda4730323d62a9
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182 plt.xticks(numpy.arange(0, maximumX + 1, 1.0))
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ea67840d0514 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 797ff8e0461392fe4542de33e7b58f9e0abefc7c
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183 plt.ylim((0, maximumY * 1.2))
1
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184
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185 legend = "sample size= {:,} against {:,}".format(len(ham[0]), lenTags, lenTags)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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186 plt.text(0.14, -0.01, legend, size=12, transform=plt.gcf().transFigure)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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187 pdf.savefig(fig, bbox_inches="tight")
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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188 plt.close("all")
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189 plt.clf()
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190
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191 def createTableFSD2(list1, diff=True):
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192 selfAB = numpy.concatenate(list1)
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193 uniqueFS = numpy.unique(selfAB)
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194 nr = numpy.arange(0, len(uniqueFS), 1)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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195 if diff is False:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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196 count = numpy.zeros((len(uniqueFS), 6))
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197 else:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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198 count = numpy.zeros((len(uniqueFS), 7))
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199
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200 state = 1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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201 for i in list1:
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202 counts = list(Counter(i).items())
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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203 hd = [item[0] for item in counts]
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204 c = [item[1] for item in counts]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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205 table = numpy.column_stack((hd, c))
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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206 if len(table) == 0:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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207 state = state + 1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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208 continue
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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209 else:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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210 if state == 1:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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211 for i, l in zip(uniqueFS, nr):
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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212 for j in table:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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213 if j[0] == uniqueFS[l]:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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diff changeset
214 count[l, 0] = j[1]
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215 if state == 2:
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216 for i, l in zip(uniqueFS, nr):
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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217 for j in table:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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218 if j[0] == uniqueFS[l]:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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219 count[l, 1] = j[1]
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220
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221 if state == 3:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
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222 for i, l in zip(uniqueFS, nr):
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
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223 for j in table:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
224 if j[0] == uniqueFS[l]:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
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diff changeset
225 count[l, 2] = j[1]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
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226
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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227 if state == 4:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
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228 for i, l in zip(uniqueFS, nr):
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
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229 for j in table:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
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230 if j[0] == uniqueFS[l]:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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diff changeset
231 count[l, 3] = j[1]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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232
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233 if state == 5:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
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diff changeset
234 for i, l in zip(uniqueFS, nr):
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
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diff changeset
235 for j in table:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
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diff changeset
236 if j[0] == uniqueFS[l]:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
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diff changeset
237 count[l, 4] = j[1]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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238
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diff changeset
239 if state == 6:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
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240 for i, l in zip(uniqueFS, nr):
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
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diff changeset
241 for j in table:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
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diff changeset
242 if j[0] == uniqueFS[l]:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
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diff changeset
243 count[l, 5] = j[1]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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244
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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245 if state == 7:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
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246 for i, l in zip(uniqueFS, nr):
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
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diff changeset
247 for j in table:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
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diff changeset
248 if j[0] == uniqueFS[l]:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
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diff changeset
249 count[l, 6] = j[1]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
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diff changeset
250 state = state + 1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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diff changeset
251
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252 sumRow = count.sum(axis=1)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
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253 sumCol = count.sum(axis=0)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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254
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diff changeset
255 uniqueFS = uniqueFS.astype(str)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
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256 if uniqueFS[len(uniqueFS) - 1] == "20":
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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257 uniqueFS[len(uniqueFS) - 1] = ">20"
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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258
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diff changeset
259 first = ["FS={}".format(i) for i in uniqueFS]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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260 final = numpy.column_stack((first, count, sumRow))
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261
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262 return (final, sumCol)
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263
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264 def createFileFSD2(summary, sumCol, overallSum, output_file, name,sep, rel=False, diff=True):
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265 output_file.write(name)
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266 output_file.write("\n")
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267 if diff is False:
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268 output_file.write("{}HD=1{}HD=2{}HD=3{}HD=4{}HD=5-8{}HD>8{}sum{}\n".format(sep,sep,sep,sep,sep,sep,sep,sep))
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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269 else:
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270 if rel is False:
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271 output_file.write("{}diff=0{}diff=1{}diff=2{}diff=3{}diff=4{}diff=5-8{}diff>8{}sum{}\n".format(sep,sep,sep,sep,sep,sep,sep,sep,sep))
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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272 else:
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273 output_file.write("{}diff=0{}diff=0.1{}diff=0.2{}diff=0.3{}diff=0.4{}diff=0.5-0.8{}diff>0.8{}sum{}\n".format(sep,sep,sep,sep,sep,sep,sep,sep,sep))
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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274
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275 for item in summary:
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276 for nr in item:
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277 if "FS" not in nr and "diff" not in nr:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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278 nr = nr.astype(float)
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279 nr = nr.astype(int)
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280 output_file.write("{}{}".format(nr,sep))
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281 output_file.write("\n")
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282 output_file.write("sum{}".format(sep))
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283 sumCol = map(int, sumCol)
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284 for el in sumCol:
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285 output_file.write("{}{}".format(el,sep))
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286 output_file.write("{}{}".format(overallSum.astype(int),sep))
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287 output_file.write("\n\n")
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288
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289 def createTableHD(list1, row_label):
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290 selfAB = numpy.concatenate(list1)
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291 uniqueHD = numpy.unique(selfAB)
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292 nr = numpy.arange(0, len(uniqueHD), 1)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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293 count = numpy.zeros((len(uniqueHD), 6))
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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294 state = 1
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295 for i in list1:
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296 counts = list(Counter(i).items())
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297 hd = [item[0] for item in counts]
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298 c = [item[1] for item in counts]
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299 table = numpy.column_stack((hd, c))
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300 if len(table) == 0:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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301 state = state + 1
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302 continue
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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303 else:
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304 if state == 1:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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305 for i, l in zip(uniqueHD, nr):
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306 for j in table:
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307 if j[0] == uniqueHD[l]:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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308 count[l, 0] = j[1]
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309 if state == 2:
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310 for i, l in zip(uniqueHD, nr):
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311 for j in table:
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312 if j[0] == uniqueHD[l]:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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313 count[l, 1] = j[1]
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314
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315 if state == 3:
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316 for i, l in zip(uniqueHD, nr):
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317 for j in table:
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318 if j[0] == uniqueHD[l]:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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319 count[l, 2] = j[1]
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320
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321 if state == 4:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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322 for i, l in zip(uniqueHD, nr):
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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323 for j in table:
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324 if j[0] == uniqueHD[l]:
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325 count[l, 3] = j[1]
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326
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327 if state == 5:
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328 for i, l in zip(uniqueHD, nr):
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329 for j in table:
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330 if j[0] == uniqueHD[l]:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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331 count[l, 4] = j[1]
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332
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333 if state == 6:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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334 for i, l in zip(uniqueHD, nr):
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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335 for j in table:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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336 if j[0] == uniqueHD[l]:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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337 count[l, 5] = j[1]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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338 state = state + 1
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339
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340 sumRow = count.sum(axis=1)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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341 sumCol = count.sum(axis=0)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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342 first = ["{}{}".format(row_label,i) for i in uniqueHD]
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343 final = numpy.column_stack((first, count, sumRow))
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344
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345 return (final, sumCol)
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346
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347 def createTableHDwithTags(list1):
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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348 selfAB = numpy.concatenate(list1)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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349 uniqueHD = numpy.unique(selfAB)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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diff changeset
350 nr = numpy.arange(0, len(uniqueHD), 1)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
351 count = numpy.zeros((len(uniqueHD), 3))
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
352
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
353 state = 1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
354 for i in list1:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
355 counts = list(Counter(i).items())
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
356 hd = [item[0] for item in counts]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
357 c = [item[1] for item in counts]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
358 table = numpy.column_stack((hd, c))
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
359 if len(table) == 0:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
360 state = state + 1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
361 continue
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
362 else:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
363 if state == 1:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
364 for i, l in zip(uniqueHD, nr):
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
365 for j in table:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
366 if j[0] == uniqueHD[l]:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
367 count[l, 0] = j[1]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
368 if state == 2:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
369 for i, l in zip(uniqueHD, nr):
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
370 for j in table:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
371 if j[0] == uniqueHD[l]:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
372 count[l, 1] = j[1]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
373
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
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diff changeset
374 if state == 3:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
375 for i, l in zip(uniqueHD, nr):
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
376 for j in table:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
377 if j[0] == uniqueHD[l]:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
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diff changeset
378 count[l, 2] = j[1]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
379 state = state + 1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
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diff changeset
380
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
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diff changeset
381 sumRow = count.sum(axis=1)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
382 sumCol = count.sum(axis=0)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
383 first = ["HD={}".format(i) for i in uniqueHD]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
384 final = numpy.column_stack((first, count, sumRow))
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
385
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
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diff changeset
386 return (final, sumCol)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
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387
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
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diff changeset
388 def createFileHD(summary, sumCol, overallSum, output_file, name,sep):
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
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diff changeset
389 output_file.write(name)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
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diff changeset
390 output_file.write("\n")
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
391 output_file.write("{}FS=1{}FS=2{}FS=3{}FS=4{}FS=5-10{}FS>10{}sum{}\n".format(sep,sep,sep,sep,sep,sep,sep,sep))
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
392 for item in summary:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
393 for nr in item:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
394 if "HD" not in nr and "diff" not in nr:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
395 nr = nr.astype(float)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
396 nr = nr.astype(int)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
397 output_file.write("{}{}".format(nr,sep))
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
398 output_file.write("\n")
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
399 output_file.write("sum{}".format(sep))
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
400 sumCol = map(int, sumCol)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
401 for el in sumCol:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
402 output_file.write("{}{}".format(el,sep))
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
403 output_file.write("{}{}".format(overallSum.astype(int),sep))
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
404 output_file.write("\n\n")
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
405
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
406 def createFileHDwithinTag(summary, sumCol, overallSum, output_file, name,sep):
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
407 output_file.write(name)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
408 output_file.write("\n")
2
316fbf91dd12 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit f9d5547849dabb59a33a5e998bda4730323d62a9
mheinzl
parents: 1
diff changeset
409 output_file.write("{}HD a+b;HD a{}HD b{}sum{}\n".format(sep,sep,sep,sep))
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
410 for item in summary:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
411 for nr in item:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
412 if "HD" not in nr:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
413 nr = nr.astype(float)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
414 nr = nr.astype(int)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
415 output_file.write("{}{}".format(nr,sep))
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
416 output_file.write("\n")
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
417 output_file.write("sum{}".format(sep))
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
418 sumCol = map(int, sumCol)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
419 for el in sumCol:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
420 output_file.write("{}{}".format(el,sep))
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
421 output_file.write("{}{}".format(overallSum.astype(int),sep))
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
422 output_file.write("\n\n")
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
423
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
424 def hamming(array1, array2):
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
425 res = 99 * numpy.ones(len(array1))
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
426 i = 0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
427 array2 = numpy.unique(array2) # remove duplicate sequences to decrease running time
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
428 for a in array1:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
429 dist = numpy.array([sum(itertools.imap(operator.ne, a, b)) for b in array2]) # fastest
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
430 res[i] = numpy.amin(dist[dist > 0]) # pick min distance greater than zero
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
431 #print(i)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
432 i += 1
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
433 return res
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
434
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
435 def hamming_difference(array1, array2, mate_b):
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
436 array2 = numpy.unique(array2) # remove duplicate sequences to decrease running time
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
437 array1_half = numpy.array([i[0:(len(i)) / 2] for i in array1]) # mate1 part1
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
438 array1_half2 = numpy.array([i[len(i) / 2:len(i)] for i in array1]) # mate1 part 2
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
439
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
440 array2_half = numpy.array([i[0:(len(i)) / 2] for i in array2]) # mate2 part1
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
441 array2_half2 = numpy.array([i[len(i) / 2:len(i)] for i in array2]) # mate2 part2
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
442
8
e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a
mheinzl
parents: 7
diff changeset
443 #diff11 = 999 * numpy.ones(len(array2))
e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a
mheinzl
parents: 7
diff changeset
444 #relativeDiffList = 999 * numpy.ones(len(array2))
e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a
mheinzl
parents: 7
diff changeset
445 #ham1 = 999 * numpy.ones(len(array2))
e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a
mheinzl
parents: 7
diff changeset
446 #ham2 = 999 * numpy.ones(len(array2))
e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a
mheinzl
parents: 7
diff changeset
447 #min_valueList = 999 * numpy.ones(len(array2))
e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a
mheinzl
parents: 7
diff changeset
448 #min_tagsList = 999 * numpy.ones(len(array2))
e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a
mheinzl
parents: 7
diff changeset
449 #diff11_zeros = 999 * numpy.ones(len(array2))
e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a
mheinzl
parents: 7
diff changeset
450 #min_tagsList_zeros = 999 * numpy.ones(len(array2))
2
316fbf91dd12 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit f9d5547849dabb59a33a5e998bda4730323d62a9
mheinzl
parents: 1
diff changeset
451
316fbf91dd12 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit f9d5547849dabb59a33a5e998bda4730323d62a9
mheinzl
parents: 1
diff changeset
452
8
e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a
mheinzl
parents: 7
diff changeset
453 diff11 = []
e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a
mheinzl
parents: 7
diff changeset
454 relativeDiffList = []
e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a
mheinzl
parents: 7
diff changeset
455 ham1 = []
e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a
mheinzl
parents: 7
diff changeset
456 ham2 = []
14
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
457 ham1min = []
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
458 ham2min = []
8
e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a
mheinzl
parents: 7
diff changeset
459 min_valueList = []
e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a
mheinzl
parents: 7
diff changeset
460 min_tagsList = []
e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a
mheinzl
parents: 7
diff changeset
461 diff11_zeros = []
e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a
mheinzl
parents: 7
diff changeset
462 min_tagsList_zeros = []
e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a
mheinzl
parents: 7
diff changeset
463 i = 0 # counter, only used to see how many HDs of tags were already calculated
0
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 mate_b is False: # HD calculation for all a's
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
465 half1_mate1 = array1_half
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
466 half2_mate1 = array1_half2
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
467 half1_mate2 = array2_half
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
468 half2_mate2 = array2_half2
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
469 elif mate_b is True: # HD calculation for all b's
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
470 half1_mate1 = array1_half2
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
471 half2_mate1 = array1_half
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
472 half1_mate2 = array2_half2
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
473 half2_mate2 = array2_half
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
474
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
475 for a, b, tag in zip(half1_mate1, half2_mate1, array1):
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
476 ## exclude identical tag from array2, to prevent comparison to itself
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
477 sameTag = numpy.where(array2 == tag)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
478 indexArray2 = numpy.arange(0, len(array2), 1)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
479 index_withoutSame = numpy.delete(indexArray2, sameTag) # delete identical tag from the data
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
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 # all tags without identical tag
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
482 array2_half_withoutSame = half1_mate2[index_withoutSame]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
483 array2_half2_withoutSame = half2_mate2[index_withoutSame]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
484 #array2_withoutSame = array2[index_withoutSame] # whole tag (=not splitted into 2 halfs)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
485
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
486 dist = numpy.array([sum(itertools.imap(operator.ne, a, c)) for c in
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
487 array2_half_withoutSame]) # calculate HD of "a" in the tag to all "a's" or "b" in the tag to all "b's"
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
488 min_index = numpy.where(dist == dist.min()) # get index of min HD
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
489 min_value = dist[min_index] # get minimum HDs
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
490 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
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
491 #min_tag = array2_withoutSame[min_index] # get whole tag with min HD
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
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 dist2 = numpy.array([sum(itertools.imap(operator.ne, b, e)) for e in
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
494 min_tag_half2]) # calculate HD of "b" to all "b's" or "a" to all "a's"
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
495 for d_1, d_2 in zip(min_value, dist2):
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
496 if mate_b is True: # half2, corrects the variable of the HD from both halfs if it is a or b
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
497 d = d_2
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
498 d2 = d_1
14
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mheinzl
parents: 13
diff changeset
499 ham2.append(d)
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
500 ham2min.append(d2)
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
501 else: # half1, corrects the variable of the HD from both halfs if it is a or b
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
502 d = d_1
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
503 d2 = d_2
14
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
504 ham1.append(d)
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
505 ham1min.append(d2)
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
506
8
e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a
mheinzl
parents: 7
diff changeset
507 min_valueList.append(d + d2)
e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a
mheinzl
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diff changeset
508 min_tagsList.append(tag)
14
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
509 # ham1.append(d)
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
510 # ham2.append(d2)
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
511 difference1 = abs(d - d2)
8
e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a
mheinzl
parents: 7
diff changeset
512 diff11.append(difference1)
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
513 rel_difference = round(float(difference1) / (d + d2), 1)
8
e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a
mheinzl
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diff changeset
514 relativeDiffList.append(rel_difference)
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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 #### tags which have identical parts:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
517 if d == 0 or d2 == 0:
8
e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a
mheinzl
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diff changeset
518 min_tagsList_zeros.append(tag)
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
519 difference1_zeros = abs(d - d2)
8
e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a
mheinzl
parents: 7
diff changeset
520 diff11_zeros.append(difference1_zeros)
e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a
mheinzl
parents: 7
diff changeset
521 i += 1
2
316fbf91dd12 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit f9d5547849dabb59a33a5e998bda4730323d62a9
mheinzl
parents: 1
diff changeset
522
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
523 #print(i)
11
7adc48c8a03d planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 8d9bdadb5e154dadc455720c99700afbd9aafae9
mheinzl
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diff changeset
524 #diff11 = [st for st in diff11 if st != 999]
7adc48c8a03d planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 8d9bdadb5e154dadc455720c99700afbd9aafae9
mheinzl
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diff changeset
525 #ham1 = [st for st in ham1 if st != 999]
7adc48c8a03d planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 8d9bdadb5e154dadc455720c99700afbd9aafae9
mheinzl
parents: 10
diff changeset
526 #ham2 = [st for st in ham2 if st != 999]
7adc48c8a03d planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 8d9bdadb5e154dadc455720c99700afbd9aafae9
mheinzl
parents: 10
diff changeset
527 #min_valueList = [st for st in min_valueList if st != 999]
7adc48c8a03d planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 8d9bdadb5e154dadc455720c99700afbd9aafae9
mheinzl
parents: 10
diff changeset
528 #min_tagsList = [st for st in min_tagsList if st != 999]
7adc48c8a03d planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 8d9bdadb5e154dadc455720c99700afbd9aafae9
mheinzl
parents: 10
diff changeset
529 #relativeDiffList = [st for st in relativeDiffList if st != 999]
7adc48c8a03d planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 8d9bdadb5e154dadc455720c99700afbd9aafae9
mheinzl
parents: 10
diff changeset
530 #diff11_zeros = [st for st in diff11_zeros if st != 999]
7adc48c8a03d planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 8d9bdadb5e154dadc455720c99700afbd9aafae9
mheinzl
parents: 10
diff changeset
531 #min_tagsList_zeros = [st for st in min_tagsList_zeros if st != 999]
2
316fbf91dd12 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit f9d5547849dabb59a33a5e998bda4730323d62a9
mheinzl
parents: 1
diff changeset
532
14
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
533 return ([diff11, ham1, ham2, min_valueList, min_tagsList, relativeDiffList, diff11_zeros, min_tagsList_zeros, ham1min, ham2min])
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
534
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
535 def readFileReferenceFree(file):
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
536 with open(file, 'r') as dest_f:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
537 data_array = numpy.genfromtxt(dest_f, skip_header=0, delimiter='\t', comments='#', dtype='string')
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
538 integers = numpy.array(data_array[:, 0]).astype(int)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
539 return(integers, data_array)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
540
11
7adc48c8a03d planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 8d9bdadb5e154dadc455720c99700afbd9aafae9
mheinzl
parents: 10
diff changeset
541 def hammingDistanceWithFS(fs, ham):
7adc48c8a03d planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 8d9bdadb5e154dadc455720c99700afbd9aafae9
mheinzl
parents: 10
diff changeset
542 fs = numpy.asarray(fs)
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
543 maximum = max(ham)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
544 minimum = min(ham)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
545 ham = numpy.asarray(ham)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
546
11
7adc48c8a03d planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 8d9bdadb5e154dadc455720c99700afbd9aafae9
mheinzl
parents: 10
diff changeset
547 singletons = numpy.where(fs == 1)[0]
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
548 data = ham[singletons]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
549
11
7adc48c8a03d planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 8d9bdadb5e154dadc455720c99700afbd9aafae9
mheinzl
parents: 10
diff changeset
550 hd2 = numpy.where(fs == 2)[0]
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
551 data2 = ham[hd2]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
552
11
7adc48c8a03d planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 8d9bdadb5e154dadc455720c99700afbd9aafae9
mheinzl
parents: 10
diff changeset
553 hd3 = numpy.where(fs == 3)[0]
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
554 data3 = ham[hd3]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
555
11
7adc48c8a03d planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 8d9bdadb5e154dadc455720c99700afbd9aafae9
mheinzl
parents: 10
diff changeset
556 hd4 = numpy.where(fs == 4)[0]
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
557 data4 = ham[hd4]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
558
11
7adc48c8a03d planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 8d9bdadb5e154dadc455720c99700afbd9aafae9
mheinzl
parents: 10
diff changeset
559 hd5 = numpy.where((fs >= 5) & (fs <= 10))[0]
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
560 data5 = ham[hd5]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
561
11
7adc48c8a03d planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 8d9bdadb5e154dadc455720c99700afbd9aafae9
mheinzl
parents: 10
diff changeset
562 hd6 = numpy.where(fs > 10)[0]
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
563 data6 = ham[hd6]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
564
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
565 list1 = [data, data2, data3, data4, data5, data6]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
566 return(list1, maximum, minimum)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
567
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
568 def familySizeDistributionWithHD(fs, ham, diff=False, rel = True):
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
569 hammingDistances = numpy.unique(ham)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
570 fs = numpy.asarray(fs)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
571
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
572 ham = numpy.asarray(ham)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
573 bigFamilies2 = numpy.where(fs > 19)[0]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
574 if len(bigFamilies2) != 0:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
575 fs[bigFamilies2] = 20
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
576 maximum = max(fs)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
577 minimum = min(fs)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
578 if diff is True:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
579 hd0 = numpy.where(ham == 0)[0]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
580 data0 = fs[hd0]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
581
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
582 if rel is True:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
583 hd1 = numpy.where(ham == 0.1)[0]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
584 else:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
585 hd1 = numpy.where(ham == 1)[0]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
586 data = fs[hd1]
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 if rel is True:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
589 hd2 = numpy.where(ham == 0.2)[0]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
590 else:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
591 hd2 = numpy.where(ham == 2)[0]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
592 data2 = fs[hd2]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
593
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
594 if rel is True:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
595 hd3 = numpy.where(ham == 0.3)[0]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
596 else:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
597 hd3 = numpy.where(ham == 3)[0]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
598 data3 = fs[hd3]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
599
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
600 if rel is True:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
601 hd4 = numpy.where(ham == 0.4)[0]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
602 else:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
603 hd4 = numpy.where(ham == 4)[0]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
604 data4 = fs[hd4]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
605
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
606 if rel is True:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
607 hd5 = numpy.where((ham >= 0.5) & (ham <= 0.8))[0]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
608 else:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
609 hd5 = numpy.where((ham >= 5) & (ham <= 8))[0]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
610 data5 = fs[hd5]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
611
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
612 if rel is True:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
613 hd6 = numpy.where(ham > 0.8)[0]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
614 else:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
615 hd6 = numpy.where(ham > 8)[0]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
616 data6 = fs[hd6]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
617
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
618 if diff is True:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
619 list1 = [data0,data, data2, data3, data4, data5, data6]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
620 else:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
621 list1 = [data, data2, data3, data4, data5, data6]
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 return(list1, hammingDistances, maximum, minimum)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
624
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
625 def make_argparser():
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
626 parser = argparse.ArgumentParser(description='Hamming distance analysis of duplex sequencing data')
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
627 parser.add_argument('--inputFile',
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
628 help='Tabular File with three columns: ab or ba, tag and family size.')
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
629 parser.add_argument('--inputName1')
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
630 parser.add_argument('--inputFile2',default=None,
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
631 help='Tabular File with three columns: ab or ba, tag and family size.')
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
632 parser.add_argument('--inputName2')
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
633 parser.add_argument('--sample_size', default=1000,type=int,
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
634 help='Sample size of Hamming distance analysis.')
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
635 parser.add_argument('--sep', default=",",
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
636 help='Separator in the csv file.')
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
637 parser.add_argument('--subset_tag', default=0,type=int,
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
638 help='The tag is shortened to the given number.')
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
639 parser.add_argument('--nproc', default=4,type=int,
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
640 help='The tool runs with the given number of processors.')
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
641 parser.add_argument('--only_DCS', action="store_false", # default=False, type=bool,
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
642 help='Only tags of the DCSs are included in the HD analysis')
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
643
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
644 parser.add_argument('--minFS', default=1, type=int,
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
645 help='Only tags, which have a family size greater or equal than specified, are included in the HD analysis')
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
646 parser.add_argument('--maxFS', default=0, type=int,
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
647 help='Only tags, which have a family size smaller or equal than specified, are included in the HD analysis')
14
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mheinzl
parents: 13
diff changeset
648 parser.add_argument('--nr_above_bars', action="store_true", # default=False, type=bool,
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
649 help='If no, values above bars in the histrograms are removed')
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
650
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
651 parser.add_argument('--output_csv', default="data.csv", type=str,
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
652 help='Name of the csv file.')
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
653 parser.add_argument('--output_pdf', default="data.pdf", type=str,
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
654 help='Name of the pdf file.')
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
655 parser.add_argument('--output_pdf2', default="data2.pdf", type=str,
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
656 help='Name of the pdf file.')
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
657 parser.add_argument('--output_csv2', default="data2.csv", type=str,
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
658 help='Name of the csv file.')
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
659
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
660 return parser
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
661
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
662 def Hamming_Distance_Analysis(argv):
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
663 parser = make_argparser()
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
664 args = parser.parse_args(argv[1:])
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
665
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
666 file1 = args.inputFile
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
667 name1 = args.inputName1
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
668
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
669 file2 = args.inputFile2
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
670 name2 = args.inputName2
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
671
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
672 index_size = args.sample_size
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
673 title_savedFile_pdf = args.output_pdf
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
674 title_savedFile_pdf2 = args.output_pdf2
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
675
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
676 title_savedFile_csv = args.output_csv
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
677 title_savedFile_csv2 = args.output_csv2
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
678
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
679 sep = args.sep
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
680 onlyDuplicates = args.only_DCS
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
681 minFS = args.minFS
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
682 maxFS = args.maxFS
14
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mheinzl
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diff changeset
683 nr_above_bars = args.nr_above_bars
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
684
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
685
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
686 subset = args.subset_tag
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
687 nproc = args.nproc
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
688
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
689 ### input checks
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
690 if index_size < 0:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
691 print("index_size is a negative integer.")
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
692 exit(2)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
693
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
694 if nproc <= 0:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
695 print("nproc is smaller or equal zero")
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
696 exit(3)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
697
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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parents:
diff changeset
698 if type(sep) is not str or len(sep)>1:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
699 print("sep must be a single character.")
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
700 exit(4)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
701
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
702 if subset < 0:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
703 print("subset_tag is smaller or equal zero.")
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
704 exit(5)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
705
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
706 ### PLOT ###
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
707 plt.rcParams['axes.facecolor'] = "E0E0E0" # grey background color
10
69aa17354a6e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit f01678e9bfead9f9e1b54dd9ecf7141f057dd9de
mheinzl
parents: 9
diff changeset
708 plt.rcParams['xtick.labelsize'] = 14
69aa17354a6e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit f01678e9bfead9f9e1b54dd9ecf7141f057dd9de
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diff changeset
709 plt.rcParams['ytick.labelsize'] = 14
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
710 plt.rcParams['patch.edgecolor'] = "#000000"
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
711 plt.rc('figure', figsize=(11.69, 8.27)) # A4 format
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
712
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
713 if file2 != str(None):
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
714 files = [file1, file2]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
715 name1 = name1.split(".tabular")[0]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
716 name2 = name2.split(".tabular")[0]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
717 names = [name1, name2]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
718 pdf_files = [title_savedFile_pdf, title_savedFile_pdf2]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
719 csv_files = [title_savedFile_csv, title_savedFile_csv2]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
720 else:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
721 files = [file1]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
722 name1 = name1.split(".tabular")[0]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
723 names = [name1]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
724 pdf_files = [title_savedFile_pdf]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
725 csv_files = [title_savedFile_csv]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
726
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
727 for f, name_file, pdf_f, csv_f in zip(files, names, pdf_files, csv_files):
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
728 with open(csv_f, "w") as output_file, PdfPages(pdf_f) as pdf:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
729 print("dataset: ", name_file)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
730 integers, data_array = readFileReferenceFree(f)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
731 data_array = numpy.array(data_array)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
732 int_f = numpy.array(data_array[:, 0]).astype(int)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
733 data_array = data_array[numpy.where(int_f >= minFS)]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
734 integers = integers[integers >= minFS]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
735
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
736 # select family size for tags
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
737 if maxFS > 0:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
738 int_f2 = numpy.array(data_array[:, 0]).astype(int)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
739 data_array = data_array[numpy.where(int_f2 <= maxFS)]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
740 integers = integers[integers <= maxFS]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
741
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
742 print("min FS", min(integers))
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
743 print("max FS", max(integers))
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
744
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
745 tags = data_array[:, 2]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
746 seq = data_array[:, 1]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
747
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
748 if onlyDuplicates is True:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
749 # find all unique tags and get the indices for ALL tags, but only once
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
750 u, index_unique, c = numpy.unique(numpy.array(seq), return_counts=True, return_index=True)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
751 d = u[c > 1]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
752
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
753 # get family sizes, tag for duplicates
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
754 duplTags_double = integers[numpy.in1d(seq, d)]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
755 duplTags = duplTags_double[0::2] # ab of DCS
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
756 duplTagsBA = duplTags_double[1::2] # ba of DCS
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
757
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
758 duplTags_tag = tags[numpy.in1d(seq, d)][0::2] # ab
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
759 duplTags_seq = seq[numpy.in1d(seq, d)][0::2] # ab - tags
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
760
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
761 data_array = numpy.column_stack((duplTags, duplTags_seq))
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
762 data_array = numpy.column_stack((data_array, duplTags_tag))
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
763 integers = numpy.array(data_array[:, 0]).astype(int)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
764 print("DCS in whole dataset", len(data_array))
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
765
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
766 ## HD analysis for a subset of the tag
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
767 if subset > 0:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
768 tag1 = numpy.array([i[0:(len(i)) / 2] for i in data_array[:, 1]])
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
769 tag2 = numpy.array([i[len(i) / 2:len(i)] for i in data_array[:, 1]])
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
770
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
771 flanking_region_float = float((len(tag1[0]) - subset)) / 2
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
772 flanking_region = int(flanking_region_float)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
773 if flanking_region_float % 2 == 0:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
774 tag1_shorten = numpy.array([i[flanking_region:len(i) - flanking_region] for i in tag1])
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
775 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
mheinzl
parents:
diff changeset
776 else:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
777 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
parents:
diff changeset
778 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
parents:
diff changeset
779 tag1_shorten = numpy.array(
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
780 [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:
diff changeset
781 tag2_shorten = numpy.array(
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
782 [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
mheinzl
parents:
diff changeset
783
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
784 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
parents:
diff changeset
785 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
mheinzl
parents:
diff changeset
786
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
787 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
mheinzl
parents:
diff changeset
788 # 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
parents:
diff changeset
789 if index_size == 0:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
790 result = numpy.arange(0, len(data_array), 1)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
791 else:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
792 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
mheinzl
parents:
diff changeset
793 replace=False) # array of random sequences of size=index.size
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
794
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
795 # 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
mheinzl
parents:
diff changeset
796 # pickle.dump(result, o, pickle.HIGHEST_PROTOCOL)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
797
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
798 # comparison random tags to whole dataset
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
799 result1 = data_array[result, 1] # random tags
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
800 result2 = data_array[:, 1] # all tags
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
801 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
parents:
diff changeset
802 print("sample size= ", len(result1))
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
803
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
804 # HD analysis of whole tag
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
805 proc_pool = Pool(nproc)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
806 chunks_sample = numpy.array_split(result1, nproc)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
807 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
parents:
diff changeset
808 proc_pool.close()
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
809 proc_pool.join()
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
810 ham = numpy.concatenate(ham).astype(int)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
811 # 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
812 # for h, tag in zip(ham, result1):
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
813 # 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
814
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
815 # 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
816 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
817 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
818 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
819 proc_pool_b.close()
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
820 proc_pool_b.join()
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
821 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
822 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
823 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
parents:
diff changeset
824 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
825 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
826 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
827 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
parents:
diff changeset
828 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
829 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
830 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
831 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
832 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
833 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
834 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
835 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
836 numpy.concatenate([item_b[7] for item_b in diff_list_b])))
14
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
837 HDhalf1min = numpy.concatenate((numpy.concatenate([item[8] for item in diff_list_a]),
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
838 numpy.concatenate([item_b[8] for item_b in diff_list_b]))).astype(int)
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
839 HDhalf2min = numpy.concatenate((numpy.concatenate([item[9] for item in diff_list_a]),
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
840 numpy.concatenate([item_b[9] for item_b in diff_list_b]))).astype(int)
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
841 # 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
842 # 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
843 # output_file2.write(
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
844 # "{}\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
mheinzl
parents:
diff changeset
845
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
846 lenTags = len(data_array)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
847
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
848 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
849 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
850 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
mheinzl
parents:
diff changeset
851
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
852 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
853 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
854 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
855 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
856
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
857 # prepare data for different kinds of plots
2
316fbf91dd12 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit f9d5547849dabb59a33a5e998bda4730323d62a9
mheinzl
parents: 1
diff changeset
858 # distribution of FSs separated after HD
316fbf91dd12 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit f9d5547849dabb59a33a5e998bda4730323d62a9
mheinzl
parents: 1
diff changeset
859 familySizeList1, hammingDistances, maximumXFS, minimumXFS = familySizeDistributionWithHD(quant, ham,rel=False)
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
860 list1, maximumX, minimumX = hammingDistanceWithFS(quant, ham) # histogram of HDs separated after FS
2
316fbf91dd12 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit f9d5547849dabb59a33a5e998bda4730323d62a9
mheinzl
parents: 1
diff changeset
861
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
862 ## 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
863 # 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
parents:
diff changeset
864 seqDic = dict(zip(seq, quant))
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
865 lst_minHD_tags = []
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
866 for i in minHD_tags:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
867 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
868
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
869 # 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
parents:
diff changeset
870 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
parents:
diff changeset
871 listRelDifference1, maximumXRelDifference, minimumXRelDifference = hammingDistanceWithFS(lst_minHD_tags,
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
872 rel_Diff)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
873
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
874 # 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
parents:
diff changeset
875 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
parents:
diff changeset
876 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
parents:
diff changeset
877 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
parents:
diff changeset
878 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
parents:
diff changeset
879
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
880 # 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
parents:
diff changeset
881 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
882 lst_minHD_tags_zeros = []
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
883 for i in minHD_tags_zeros:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
884 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
parents:
diff changeset
885
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
886 # histogram with HD of non-identical half
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
887 listDifference1_zeros, maximumXDifference_zeros, minimumXDifference_zeros = hammingDistanceWithFS(
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
888 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
889 # family size distribution of non-identical half
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
890 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
parents:
diff changeset
891 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
parents:
diff changeset
892
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
893 #####################################################################################################################
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
894 ################## 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
895 #####################################################################################################################
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
896 plotHDwithFSD(list1=list1, maximumX=maximumX, minimumX=minimumX, pdf=pdf,
2
316fbf91dd12 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit f9d5547849dabb59a33a5e998bda4730323d62a9
mheinzl
parents: 1
diff changeset
897 subtitle="Hamming distance separated by family size", title_file1=name_file,
14
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
898 lenTags=lenTags,xlabel="HD", nr_above_bars=nr_above_bars)
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
899
14
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
900 ########################## Plot FSD with separation after ###############################################
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
901 ######################################################################################################################
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
902 plotFSDwithHD2(familySizeList1, maximumXFS, minimumXFS,
11
7adc48c8a03d planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 8d9bdadb5e154dadc455720c99700afbd9aafae9
mheinzl
parents: 10
diff changeset
903 originalCounts=quant, subtitle="Family size distribution separated by Hamming distance",
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
904 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
parents:
diff changeset
905
14
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
906 ########################## Plot HD within tags ########################################################
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
907 ######################################################################################################################
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
908 # plotHDwithinSeq_Sum2(HDhalf1, HDhalf2, minHDs, pdf=pdf, lenTags=lenTags, title_file1=name_file)
16
ea67840d0514 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 797ff8e0461392fe4542de33e7b58f9e0abefc7c
mheinzl
parents: 15
diff changeset
909 plotHDwithinSeq_Sum2(HDhalf1, HDhalf1min,HDhalf2, HDhalf2min , minHDs, pdf=pdf, lenTags=lenTags, title_file1=name_file)
14
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
910
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
911
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
912 ########################## Plot difference between HD's separated after FSD ####################################
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
913 ######################################################################################################################
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
914 plotHDwithFSD(listDifference1, maximumXDifference, minimumXDifference, pdf=pdf,
2
316fbf91dd12 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit f9d5547849dabb59a33a5e998bda4730323d62a9
mheinzl
parents: 1
diff changeset
915 subtitle="Delta Hamming distance within tags",
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
916 title_file1=name_file, lenTags=lenTags,
14
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
917 xlabel="absolute delta HD", relative=False, nr_above_bars=nr_above_bars)
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
918
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
919 plotHDwithFSD(listRelDifference1, maximumXRelDifference, minimumXRelDifference, pdf=pdf,
14
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
920 subtitle="Chimera Analysis: relative delta Hamming distances",
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
921 title_file1=name_file, lenTags=lenTags,
14
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
922 xlabel="relative delta HD", relative=True, nr_above_bars=nr_above_bars)
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
923
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
924 #################### 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
925 ########################################################################################################################
14
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
926 # plotFSDwithHD2(familySizeList1_diff, maximumXFS_diff, minimumXFS_diff,
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
927 # subtitle="Family size distribution separated by delta Hamming distances within the tags",
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
928 # pdf=pdf,relative=False, diff=True, title_file1=name_file, originalCounts=quant)
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
929
14
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
930 # plotFSDwithHD2(familySizeList1_reldiff, maximumXFS_reldiff, minimumXFS_reldiff, originalCounts=quant, pdf=pdf,
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
931 # subtitle="Family size distribution separated by delta Hamming distances within the tags",
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
932 # relative=True, diff=True, title_file1=name_file)
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
933
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
934
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
935 # plots for chimeric reads
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
936 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
937 ## HD
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
938 plotHDwithFSD(listDifference1_zeros, maximumXDifference_zeros, minimumXDifference_zeros, pdf=pdf,
2
316fbf91dd12 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit f9d5547849dabb59a33a5e998bda4730323d62a9
mheinzl
parents: 1
diff changeset
939 subtitle="Hamming distance of the non-identical half of chimeras",
14
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
940 title_file1=name_file, lenTags=lenTags,xlabel="HD", relative=False, nr_above_bars=nr_above_bars)
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
941
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
942 ## FSD
14
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
943 # plotFSDwithHD2(familySizeList1_diff_zeros, maximumXFS_diff_zeros, minimumXFS_diff_zeros,
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
944 # originalCounts=quant, pdf=pdf,
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
945 # subtitle="Family size distribution separated by Hamming distance of the non-identical half of chimeras",
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
946 # relative=False, diff=False, title_file1=name_file)
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
947
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
948 ### 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
949 #### HD ####
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
950 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
951 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
952
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
953 #### FSD ####
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
954 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
955 overallSum5 = sum(sumCol5)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
956
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
957 ### HD of both parts of the tag ####
13
5b0a95f205ad planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 29bc65d5627553741c83ce1f298223e2b266f7c8
mheinzl
parents: 11
diff changeset
958 summary9, sumCol9 = createTableHDwithTags([HDhalf1, HDhalf2,numpy.array(minHDs)])
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
959 overallSum9 = sum(sumCol9)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
960
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
961 ## HD
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
962 # absolute difference
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
963 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
964 overallSum11 = sum(sumCol11)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
965 # 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
966 summary13, sumCol13 = createTableHD(listRelDifference1, "diff=")
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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diff changeset
967 overallSum13 = sum(sumCol13)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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968
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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diff changeset
969 ## FSD
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
970 # absolute difference
14
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diff changeset
971 # summary19, sumCol19 = createTableFSD2(familySizeList1_diff)
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
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diff changeset
972 # overallSum19 = sum(sumCol19)
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
973 # relative difference
14
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
974 # summary21, sumCol21 = createTableFSD2(familySizeList1_reldiff)
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
975 # overallSum21 = sum(sumCol21)
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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976
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
977 # chimeric reads
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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diff changeset
978 if len(minHD_tags_zeros) != 0:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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diff changeset
979 # 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
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diff changeset
980 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
981 overallSum15 = sum(sumCol15)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
982 # absolute difference and tags where at least one half has HD=0
14
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mheinzl
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983 # summary23, sumCol23 = createTableFSD2(familySizeList1_diff_zeros, diff=False)
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
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984 # overallSum23 = sum(sumCol23)
0
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985
2
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diff changeset
986 output_file.write("{}\n".format(name_file))
0
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987 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
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diff changeset
988 numpy.concatenate(list1)), lenTags, lenTags))
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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989
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990 ### HD ###
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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diff changeset
991 createFileHD(summary, sumCol, overallSum, output_file,
2
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992 "Hamming distance separated by family size", sep)
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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993 ### FSD ###
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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diff changeset
994 createFileFSD2(summary5, sumCol5, overallSum5, output_file,
2
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995 "Family size distribution separated by Hamming distance", sep,
0
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diff changeset
996 diff=False)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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997
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diff changeset
998 count = numpy.bincount(quant)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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diff changeset
999 output_file.write("{}{}\n".format(sep, f))
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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1000 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
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1001 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
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diff changeset
1002 output_file.write(
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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diff changeset
1003 "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
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1004
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
1005 ### HD within tags ###
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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1006 output_file.write(
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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diff changeset
1007 "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
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1008 "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
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1009 output_file.write(
2
316fbf91dd12 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit f9d5547849dabb59a33a5e998bda4730323d62a9
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1010 "actual number of tags with min HD = {:,} (sample size by user = {:,})\n".format(
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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1011 len(numpy.concatenate(listDifference1)), len(numpy.concatenate(list1))))
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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1012 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
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1013
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1014 createFileHDwithinTag(summary9, sumCol9, overallSum9, output_file,
2
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1015 "Hamming distance of each half in the tag", sep)
0
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1016 createFileHD(summary11, sumCol11, overallSum11, output_file,
2
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1017 "Absolute delta Hamming distances within the tag", sep)
0
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diff changeset
1018 createFileHD(summary13, sumCol13, overallSum13, output_file,
14
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1019 "Chimera analysis: relative delta Hamming distances", sep)
0
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1020
14
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1021 # createFileFSD2(summary19, sumCol19, overallSum19, output_file,
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1022 # "Family size distribution separated by absolute delta Hamming distance",
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
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1023 # sep)
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
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1024 # createFileFSD2(summary21, sumCol21, overallSum21, output_file,
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
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1025 # "Family size distribution separated by relative delta Hamming distance",
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
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1026 # sep, rel=True)
0
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1027
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1028 if len(minHD_tags_zeros) != 0:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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1029 output_file.write(
14
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
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1030 "Chimeras:\nAll 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")
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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diff changeset
1031 createFileHD(summary15, sumCol15, overallSum15, output_file,
2
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1032 "Hamming distances of non-zero half", sep)
14
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1033 # createFileFSD2(summary23, sumCol23, overallSum23, output_file,
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
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1034 # "Family size distribution separated by Hamming distance of non-zero half",
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
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1035 # sep, diff=False)
0
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diff changeset
1036 output_file.write("\n")
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1037
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1038
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1039
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1040 if __name__ == '__main__':
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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1041 sys.exit(Hamming_Distance_Analysis(sys.argv))