annotate fsd.py @ 0:9736b9d04a0b draft

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author mheinzl
date Wed, 25 Apr 2018 08:59:17 -0400
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1 #!/usr/bin/env python
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3 # Family size distribution 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, but up to 4 files can be provided, as input.
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9 # The program produces a plot which shows the distribution of family sizes of the all SSCSs from the input files and
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10 # a CSV file with the data of the plot, as well as a TXT file with all tags of the DCS and their family sizes.
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11 # If only one file is provided, then a family size distribution, which is separated after SSCSs without a partner and DCSs, is produced.
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12 # Whereas a family size distribution with multiple data in one plot is produced, when more than one file (up to 4) is given.
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14 # USAGE: python FSD_Galaxy_1.4_commandLine_FINAL.py filename --inputFile2 filename2 --inputFile3 filename3 --inputFile4 filename4 /
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15 # --title_file outputFileName --sep "characterWhichSeparatesCSVFile"
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17 import numpy
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18 import matplotlib.pyplot as plt
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19 from matplotlib.backends.backend_pdf import PdfPages
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20 import argparse
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21 import sys
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22 import os
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23 import re
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24 from Cheetah.Template import Template
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26 def readFileReferenceFree(file):
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27 with open(file, 'r') as dest_f:
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28 data_array = numpy.genfromtxt(dest_f, skip_header=0, delimiter='\t', comments='#', dtype='string')
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29 return(data_array)
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31 def make_argparser():
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32 parser = argparse.ArgumentParser(description='Family Size Distribution of duplex sequencing data')
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33 parser.add_argument('inputFile',
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34 help='Tabular File with three columns: ab or ba, tag and family size.')
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35 parser.add_argument('--inputName1')
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36 parser.add_argument('--inputFile2',default=None,
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37 help='Tabular File with three columns: ab or ba, tag and family size.')
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38 parser.add_argument('--inputName2')
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39 parser.add_argument('--inputFile3',default=None,
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40 help='Tabular File with three columns: ab or ba, tag and family size.')
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41 parser.add_argument('--inputName3')
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42 parser.add_argument('--inputFile4',default=None,
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43 help='Tabular File with three columns: ab or ba, tag and family size.')
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44 parser.add_argument('--inputName4')
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45 parser.add_argument('--sep', default=",",
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46 help='Separator in the csv file.')
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47 parser.add_argument('--output_csv', default="data.csv",type=str,
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48 help='Name of the pdf and csv file.')
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49 parser.add_argument('--output_pdf', default="data.pdf",type=str,
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50 help='Name of the pdf and csv file.')
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51 return parser
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52
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53 def compare_read_families(argv):
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54 parser = make_argparser()
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55 args=parser.parse_args(argv[1:])
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56
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57 firstFile = args.inputFile
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58 name1 = args.inputName1
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59 secondFile = args.inputFile2
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60 name2 = args.inputName2
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61 thirdFile = args.inputFile3
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62 name3 = args.inputName3
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63 fourthFile = args.inputFile4
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64 name4 = args.inputName4
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65
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66 title_file = args.output_csv
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67 title_file2 = args.output_pdf
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68 sep = args.sep
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69
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70 if type(sep) is not str or len(sep)>1:
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71 print("Error: --sep must be a single character.")
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72 exit(4)
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73
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74 plt.rc('figure', figsize=(11.69, 8.27)) # A4 format
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75 plt.rcParams['patch.edgecolor'] = "black"
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76 plt.rcParams['axes.facecolor'] = "E0E0E0" # grey background color
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77 plt.rcParams['xtick.labelsize'] = 12
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78 plt.rcParams['ytick.labelsize'] = 12
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79
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80 list_to_plot = []
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81 label = []
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82 data_array_list = []
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83
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84 with open(title_file, "w") as output_file, PdfPages(title_file2) as pdf:
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85 fig = plt.figure()
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86 plt.subplots_adjust(bottom=0.25)
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87 if firstFile != str(None):
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88 file1 = readFileReferenceFree(firstFile)
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89 integers = numpy.array(file1[:, 0]).astype(int) ## keep original family sizes
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90
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91 # for plot: replace all big family sizes by 22
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92 data1 = numpy.array(file1[:, 0]).astype(int)
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93 bigFamilies = numpy.where(data1 > 20)[0]
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94 data1[bigFamilies] = 22
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95
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96 name1 = name1.split(".tabular")[0]
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97 list_to_plot.append(data1)
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98 label.append(name1)
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99 data_array_list.append(file1)
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100
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101 legend = "\n\n\n{}".format(name1)
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102 plt.text(0.1, 0.11, legend, size=12, transform=plt.gcf().transFigure)
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103 legend1 = "singletons:\nabsolute nr.\n{:,}".format(numpy.bincount(data1)[1])
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104 plt.text(0.4, 0.11, legend1, size=12, transform=plt.gcf().transFigure)
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105
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106 legend3 = "rel. freq\n{:.3f}".format(float(numpy.bincount(data1)[1]) / len(data1))
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107 plt.text(0.5, 0.11, legend3, size=12, transform=plt.gcf().transFigure)
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108
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109 legend4 = "family size > 20:\nabsolute nr.\n{:,}".format(
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110 numpy.bincount(data1)[len(numpy.bincount(data1)) - 1].astype(int))
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111 plt.text(0.6, 0.11, legend4, size=12, transform=plt.gcf().transFigure)
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112
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113 legend5 = "rel. freq\n{:.3f}".format(float(numpy.bincount(data1)[len(numpy.bincount(data1)) - 1]) / len(data1))
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114 plt.text(0.7, 0.11, legend5, size=12, transform=plt.gcf().transFigure)
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115
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116 legend6 = "total length\n{:,}".format(len(data1))
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117 plt.text(0.8, 0.11, legend6, size=12, transform=plt.gcf().transFigure)
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118
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119 if secondFile != str(None):
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120 file2 = readFileReferenceFree(secondFile)
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121 data2 = numpy.asarray(file2[:, 0]).astype(int)
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122 bigFamilies2 = numpy.where(data2 > 20)[0]
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123 data2[bigFamilies2] = 22
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124
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125 list_to_plot.append(data2)
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126 name2 = name2.split(".tabular")[0]
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127 label.append(name2)
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128 data_array_list.append(file2)
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129
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130 plt.text(0.1, 0.09, name2, size=12, transform=plt.gcf().transFigure)
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131
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132 legend1 = "{:,}".format(numpy.bincount(data2)[1])
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133 plt.text(0.4, 0.09, legend1, size=12, transform=plt.gcf().transFigure)
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134
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135 legend3 = "{:.3f}".format(float(numpy.bincount(data2)[1]) / len(data2))
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136 plt.text(0.5, 0.09, legend3, size=12, transform=plt.gcf().transFigure)
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137
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138 legend4 = "{:,}".format(numpy.bincount(data2)[len(numpy.bincount(data2)) - 1].astype(int))
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139 plt.text(0.6, 0.09, legend4, size=12, transform=plt.gcf().transFigure)
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140
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141 legend5 = "{:.3f}".format(float(numpy.bincount(data2)[len(numpy.bincount(data2)) - 1]) / len(data2))
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142 plt.text(0.7, 0.09, legend5, size=12, transform=plt.gcf().transFigure)
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143
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144 legend6 = "{:,}".format(len(data2))
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145 plt.text(0.8, 0.09, legend6, size=12, transform=plt.gcf().transFigure)
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146
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147 if thirdFile != str(None):
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148 file3 = readFileReferenceFree(thirdFile)
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149
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150 data3 = numpy.asarray(file3[:, 0]).astype(int)
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151 bigFamilies3 = numpy.where(data3 > 20)[0]
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152 data3[bigFamilies3] = 22
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153
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154 list_to_plot.append(data3)
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155 name3 = name3.split(".tabular")[0]
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156 label.append(name3)
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157 data_array_list.append(file3)
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158
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159 plt.text(0.1, 0.07, name3, size=12, transform=plt.gcf().transFigure)
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160
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161 legend1 = "{:,}".format(numpy.bincount(data3)[1])
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162 plt.text(0.4, 0.07, legend1, size=12, transform=plt.gcf().transFigure)
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163
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164 legend3 = "{:.3f}".format(float(numpy.bincount(data3)[1]) / len(data3))
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165 plt.text(0.5, 0.07, legend3, size=12, transform=plt.gcf().transFigure)
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166
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167 legend4 = "{:,}".format(numpy.bincount(data3)[len(numpy.bincount(data3)) - 1].astype(int))
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168 plt.text(0.6, 0.07, legend4, size=12, transform=plt.gcf().transFigure)
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169
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170 legend5 = "{:.3f}".format(float(numpy.bincount(data3)[len(numpy.bincount(data3)) - 1]) / len(data3))
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171 plt.text(0.7, 0.07, legend5, size=12, transform=plt.gcf().transFigure)
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172
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173 legend6 = "{:,}".format(len(data3))
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174 plt.text(0.8, 0.07, legend6, size=12, transform=plt.gcf().transFigure)
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175
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176 if fourthFile != str(None):
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177 file4 = readFileReferenceFree(fourthFile)
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178
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179 data4 = numpy.asarray(file4[:, 0]).astype(int)
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180 bigFamilies4 = numpy.where(data4 > 20)[0]
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181 data4[bigFamilies4] = 22
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182
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183 list_to_plot.append(data4)
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184 name4 = name4.split(".tabular")[0]
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185 label.append(name4)
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186 data_array_list.append(file4)
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187
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188 plt.text(0.1, 0.05, name4, size=12, transform=plt.gcf().transFigure)
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189
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190 legend1 = "{:,}".format(numpy.bincount(data4)[1])
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191 plt.text(0.4, 0.05, legend1, size=12, transform=plt.gcf().transFigure)
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192
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193 legend4 = "{:.3f}".format(float(numpy.bincount(data4)[1]) / len(data4))
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194 plt.text(0.5, 0.05, legend4, size=12, transform=plt.gcf().transFigure)
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195
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196 legend4 = "{:,}".format(numpy.bincount(data4)[len(numpy.bincount(data4)) - 1].astype(int))
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197 plt.text(0.6, 0.05, legend4, size=12, transform=plt.gcf().transFigure)
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198
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199 legend5 = "{:.3f}".format(float(numpy.bincount(data4)[len(numpy.bincount(data4)) - 1]) / len(data4))
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200 plt.text(0.7, 0.05, legend5, size=12, transform=plt.gcf().transFigure)
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201
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202 legend6 = "{:,}".format(len(data4))
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203 plt.text(0.8, 0.05, legend6, size=12, transform=plt.gcf().transFigure)
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204
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205 maximumX = numpy.amax(numpy.concatenate(list_to_plot))
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206 minimumX = numpy.amin(numpy.concatenate(list_to_plot))
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207
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208 counts = plt.hist(list_to_plot, bins=range(minimumX, maximumX + 1), stacked=False, edgecolor="black",
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
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209 linewidth=1, label=label, align="left", alpha=0.7, rwidth=0.8)
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210
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211 ticks = numpy.arange(minimumX - 1, maximumX, 1)
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212 ticks1 = map(str, ticks)
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213 ticks1[len(ticks1) - 1] = ">20"
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214 plt.xticks(numpy.array(ticks), ticks1)
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215
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216 plt.legend(loc='upper right', fontsize=14, frameon=True, bbox_to_anchor=(0.9, 1))
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217 plt.title("Family Size Distribution", fontsize=14)
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218 plt.xlabel("No. of Family Members", fontsize=14)
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219 plt.ylabel("Absolute Frequency", fontsize=14)
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220 plt.margins(0.01, None)
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221 plt.grid(b=True, which="major", color="#424242", linestyle=":")
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222 pdf.savefig(fig)
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223 plt.close()
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224
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225 # write data to CSV file
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226 output_file.write("Values from family size distribution with all datasets\n")
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227 output_file.write("\nFamily size")
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228 for i in label:
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229 output_file.write("{}{}".format(sep, i))
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230 output_file.write("{}sum".format(sep))
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231 output_file.write("\n")
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232 j = 0
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233 for fs in counts[1][0:len(counts[1]) - 1]:
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
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234 if fs == 21:
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235 fs = ">20"
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236 else:
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237 fs = "={}".format(fs)
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238 output_file.write("FS{}{}".format(fs, sep))
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239 values_of_fs = []
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240 if len(label) == 1:
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241 output_file.write("{}{}".format(int(counts[0][j]), sep))
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
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242 values_of_fs.append(int(counts[0][j]))
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243 else:
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244 for n in range(len(label)):
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245 output_file.write("{}{}".format(int(counts[0][n][j]), sep))
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246 values_of_fs.append(int(counts[0][n][j]))
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247 output_file.write("{}\n".format(sum(values_of_fs)))
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248 j += 1
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249 output_file.write("sum{}".format(sep))
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250 values_for_sum = []
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251 if len(label) == 1:
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252 output_file.write("{}{}".format(int(sum(counts[0])), sep))
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253 values_for_sum.append(int(sum(counts[0])))
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254 else:
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255 for i in counts[0]:
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256 output_file.write("{}{}".format(int(sum(i)), sep))
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257 values_for_sum.append(int(sum(i)))
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258
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259 output_file.write("{}\n".format(sum(values_for_sum)))
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260
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261 ### Family size distribution after DCS and SSCS
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262 for dataset, data, name_file in zip(list_to_plot, data_array_list, label):
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263 maximumX = numpy.amax(dataset)
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264 minimumX = numpy.amin(dataset)
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265
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266 tags = numpy.array(data[:, 2])
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267 seq = numpy.array(data[:, 1])
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268 data = numpy.array(dataset)
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269
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270 # find all unique tags and get the indices for ALL tags, but only once
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271 u, index_unique, c = numpy.unique(numpy.array(seq), return_counts=True, return_index=True)
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272 d = u[c > 1]
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273
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274 # get family sizes, tag for duplicates
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275 duplTags_double = data[numpy.in1d(seq, d)]
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276 duplTags = duplTags_double[0::2] # ab of DCS
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277 duplTagsBA = duplTags_double[1::2] # ba of DCS
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278
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279 duplTags_double_tag = tags[numpy.in1d(seq, d)]
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280 duplTags_double_seq = seq[numpy.in1d(seq, d)]
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281
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282 # get family sizes for SSCS with no partner
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283 ab = numpy.where(tags == "ab")[0]
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284 abSeq = seq[ab]
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285 ab = data[ab]
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286 ba = numpy.where(tags == "ba")[0]
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287 baSeq = seq[ba]
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288 ba = data[ba]
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289
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290 dataAB = ab[numpy.in1d(abSeq, d, invert=True)]
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291 dataBA = ba[numpy.in1d(baSeq, d, invert=True)]
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292
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293 # write DCS tags to file
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294 # with open("DCS information_{}.txt".format(firstFile), "w") as file:
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295 # for t, s, f in zip(duplTags_double_tag, duplTags_double_seq, duplTags_double):
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296 # file.write("{}\t{}\t{}\n".format(t, s, f))
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297
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298 list1 = [duplTags_double, dataAB, dataBA] # list for plotting
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299
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300 ## information for family size >= 3
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301 dataAB_FS3 = dataAB[dataAB >= 3]
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302 dataBA_FS3 = dataBA[dataBA >= 3]
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303 ab_FS3 = ab[ab >= 3]
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304 ba_FS3 = ba[ba >= 3]
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305
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306 duplTags_FS3 = duplTags[(duplTags >= 3) & (duplTagsBA >= 3)] # ab+ba with FS>=3
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307 duplTags_FS3_BA = duplTagsBA[(duplTags >= 3) & (duplTagsBA >= 3)] # ba+ab with FS>=3
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308 duplTags_double_FS3 = len(duplTags_FS3)+len(duplTags_FS3_BA) # both ab and ba strands with FS>=3
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309
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310 fig = plt.figure()
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311
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312 plt.subplots_adjust(bottom=0.3)
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313 counts = plt.hist(list1, bins=range(minimumX, maximumX + 1), stacked=True,
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314 label=["duplex", "ab", "ba"], edgecolor="black", linewidth=1,
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315 align="left", color=["#FF0000", "#5FB404", "#FFBF00"])
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316 # tick labels of x axis
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317 ticks = numpy.arange(minimumX - 1, maximumX, 1)
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318 ticks1 = map(str, ticks)
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319 ticks1[len(ticks1) - 1] = ">20"
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320 plt.xticks(numpy.array(ticks), ticks1)
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321 singl = counts[0][2][0] # singletons
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322 last = counts[0][2][len(counts[0][0]) - 1] # large families
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323
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324 plt.legend(loc='upper right', fontsize=14, bbox_to_anchor=(0.9, 1), frameon=True)
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325 plt.title(name1, fontsize=14)
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326 plt.xlabel("No. of Family Members", fontsize=14)
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
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327 plt.ylabel("Absolute Frequency", fontsize=14)
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
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328 plt.margins(0.01, None)
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
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329 plt.grid(b=True, which="major", color="#424242", linestyle=":")
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
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330
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331 ## extra information beneath the plot
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
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332 legend = "SSCS ab= \nSSCS ba= \nDCS (total)= \nlength of dataset="
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
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333 plt.text(0.1, 0.09, legend, size=12, transform=plt.gcf().transFigure)
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
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diff changeset
334
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335 legend = "absolute numbers\n\n{:,}\n{:,}\n{:,} ({:,})\n{:,}" \
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
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336 .format(len(dataAB), len(dataBA), len(duplTags), len(duplTags_double),
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
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337 (len(dataAB) + len(dataBA) + len(duplTags)))
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
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338 plt.text(0.35, 0.09, legend, size=12, transform=plt.gcf().transFigure)
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
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339
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340 legend = "relative frequencies\nunique\n{:.3f}\n{:.3f}\n{:.3f}\n{:,}" \
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
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341 .format(float(len(dataAB)) / (len(dataAB) + len(dataBA) + len(duplTags)),
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
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342 float(len(dataBA)) / (len(dataAB) + len(dataBA) + len(duplTags)),
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
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343 float(len(duplTags)) / (len(dataAB) + len(dataBA) + len(duplTags)),
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
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344 (len(dataAB) + len(dataBA) + len(duplTags)))
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
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345 plt.text(0.54, 0.09, legend, size=12, transform=plt.gcf().transFigure)
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
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346
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347 legend = "total\n{:.3f}\n{:.3f}\n{:.3f} ({:.3f})\n{:,}" \
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
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348 .format(float(len(dataAB)) / (len(ab) + len(ba)), float(len(dataBA)) / (len(ab) + len(ba)),
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
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diff changeset
349 float(len(duplTags)) / (len(ab) + len(ba)),
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
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diff changeset
350 float(len(duplTags_double)) / (len(ab) + len(ba)), (len(ab) + len(ba)))
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
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351 plt.text(0.64, 0.09, legend, size=12, transform=plt.gcf().transFigure)
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352
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353 legend1 = "\nsingletons:\nfamily size > 20:"
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
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354 plt.text(0.1, 0.03, legend1, size=12, transform=plt.gcf().transFigure)
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
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355
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356 legend4 = "{:,}\n{:,}".format(singl.astype(int), last.astype(int))
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
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357 plt.text(0.35, 0.03, legend4, size=12, transform=plt.gcf().transFigure)
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358
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diff changeset
359 legend3 = "{:.3f}\n{:.3f}".format(singl / len(data),last / len(data))
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
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diff changeset
360 plt.text(0.54, 0.03, legend3, size=12, transform=plt.gcf().transFigure)
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
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diff changeset
361
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diff changeset
362 pdf.savefig(fig)
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
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363 plt.close()
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
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diff changeset
364
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
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365 # write same information to a csv file
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
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366 count = numpy.bincount(integers) # original counts of family sizes
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
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diff changeset
367 output_file.write("\nDataset:{}{}\n".format(sep, name_file))
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
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diff changeset
368 output_file.write("max. family size:{}{}\n".format(sep, max(integers)))
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
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diff changeset
369 output_file.write("absolute frequency:{}{}\n".format(sep, count[len(count) - 1]))
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
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diff changeset
370 output_file.write("relative frequency:{}{:.3f}\n\n".format(sep, float(count[len(count) - 1]) / sum(count)))
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
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diff changeset
371
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
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diff changeset
372 output_file.write("{}singletons:{}{}family size > 20:\n".format(sep, sep, sep))
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
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diff changeset
373 output_file.write(
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
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diff changeset
374 "{}absolute nr.{}rel. freq{}absolute nr.{}rel. freq{}total length\n".format(sep, sep, sep, sep, sep))
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
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diff changeset
375 output_file.write("{}{}{}{}{:.3f}{}{}{}{:.3f}{}{}\n\n".format(name_file, sep, singl.astype(int), sep,
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
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diff changeset
376 singl / len(data), sep,last.astype(int), sep,
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
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377 last / len(data), sep, len(data)))
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
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diff changeset
378
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
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diff changeset
379 ## information for FS >= 1
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
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diff changeset
380 output_file.write(
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
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diff changeset
381 "The unique frequencies were calculated from the dataset where the tags occured only once (=ab without DCS, ba without DCS)\n" \
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
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diff changeset
382 "Whereas the total frequencies were calculated from the whole dataset (=including the DCS).\n\n")
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
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diff changeset
383 output_file.write("FS >= 1{}{}unique:{}total:\n".format(sep, sep, sep))
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
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diff changeset
384 output_file.write("nr./rel. freq of ab={}{}{}{:.3f}{}{:.3f}\n".format(sep, len(dataAB), sep,
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
385 float(len(dataAB)) / (len(dataAB) + len(dataBA) + len( duplTags)), sep,
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
386 float(len(dataAB)) / (len(ab) + len(ba))))
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
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diff changeset
387 output_file.write("nr./rel. freq of ba={}{}{}{:.3f}{}{:.3f}\n".format(sep, len(dataBA), sep,
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
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diff changeset
388 float(len(dataBA)) / (len(dataBA) + len(dataBA) + len(duplTags)), sep,
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
389 float(len(dataBA)) / (len(ba) + len(ba))))
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
390 output_file.write(
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
391 "nr./rel. freq of DCS (total)={}{} ({}){}{:.3f}{}{:.3f} ({:.3f})\n".format(sep, len(duplTags), len(duplTags_double), sep,
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
392 float(len(duplTags)) / ( len(dataAB) + len( dataBA) + len(duplTags)),
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
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diff changeset
393 sep, float(len(duplTags)) / ( len(ab) + len(ba)),
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
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parents:
diff changeset
394 float( len(duplTags_double)) / (len(ab) + len(ba))))
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
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parents:
diff changeset
395 output_file.write(
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
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parents:
diff changeset
396 "length of dataset={}{}{}{}{}{}\n".format(sep, (len(dataAB) + len(dataBA) + len(duplTags)), sep,
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
397 (len(dataAB) + len(dataBA) + len(duplTags)), sep,(len(ab) + len(ba))))
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
398 ## information for FS >= 3
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
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diff changeset
399 output_file.write("FS >= 3{}{}unique:{}total:\n".format(sep, sep, sep))
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
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parents:
diff changeset
400 output_file.write("nr./rel. freq of ab={}{}{}{:.3f}{}{:.3f}\n".format(sep, len(dataAB_FS3), sep,
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
401 float(len(dataAB_FS3)) / (len(dataAB_FS3) + len(dataBA_FS3) + len(duplTags_FS3)),
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
402 sep, float(len(dataAB_FS3)) / ( len(ab_FS3) + len(ba_FS3))))
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
403 output_file.write("nr./rel. freq of ba={}{}{}{:.3f}{}{:.3f}\n".format(sep, len(dataBA_FS3), sep,
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
404 float(len(dataBA_FS3)) / ( len(dataBA_FS3) + len(dataBA_FS3) + len(duplTags_FS3)),
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
405 sep,float(len(dataBA_FS3)) / (len(ba_FS3) + len(ba_FS3))))
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
406 output_file.write(
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
407 "nr./rel. freq of DCS (total)={}{} ({}){}{:.3f}{}{:.3f} ({:.3f})\n".format(sep, len(duplTags_FS3),duplTags_double_FS3,
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
408 sep, float(len( duplTags_FS3)) / (len(dataBA_FS3) + len(duplTags_FS3)),
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
409 sep, float(len(duplTags_FS3)) / (len(ab_FS3) + len(ba_FS3)),
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
410 float(duplTags_double_FS3) / (len(ab_FS3) + len(ba_FS3))))
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
411 output_file.write(
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
412 "length of dataset={}{}{}{}{}{}\n".format(sep, (len(dataAB_FS3) + len(dataBA_FS3) + len(duplTags_FS3)), sep,
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
413 (len(dataAB_FS3) + len(dataBA_FS3) + len(duplTags_FS3)), sep,
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
414 (len(ab_FS3) + len(ba_FS3))))
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
415
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
416 output_file.write("\nValues from family size distribution\n")
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
417 output_file.write("{}duplex{}ab{}ba{}sum\n".format(sep, sep, sep, sep))
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
418 for dx, ab, ba, fs in zip(counts[0][0], counts[0][1], counts[0][2], counts[1]):
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
419 if fs == 21:
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
420 fs = ">20"
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
421 else:
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
422 fs = "={}".format(fs)
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
423 ab1 = ab - dx
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
424 ba1 = ba - ab
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
425 output_file.write(
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
426 "FS{}{}{}{}{}{}{}{}{}\n".format(fs, sep, int(dx), sep, int(ab1), sep, int(ba1), sep, int(ba)))
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
427
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
428 print("Files successfully created!")
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
429
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
430 if __name__ == '__main__':
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
431 sys.exit(compare_read_families(sys.argv))