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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
author mheinzl
date Thu, 10 May 2018 07:28:39 -0400
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b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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1 #!/usr/bin/env python
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3 # Family size distribution of tags which were aligned to the reference genome
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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
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9 # and a TXT with tags of reads that overlap the regions of the reference genome as input.
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10 # The program produces a plot which shows the distribution of family sizes of the tags from the input files and
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11 # a CSV file with the data of the plot.
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13 # USAGE: python FSD_regions_1.6_FINAL.py --inputFile filenameSSCS --inputName1 filenameSSCS --ref_genome filenameRefGenome --sep "characterWhichSeparatesCSVFile" --output_csv outptufile_name_csv --output_pdf outptufile_name_pdf
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15 import numpy
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16 import matplotlib.pyplot as plt
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17 import argparse
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18 import sys
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19 import os
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20 from matplotlib.backends.backend_pdf import PdfPages
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22 def readFileReferenceFree(file, delim):
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23 with open(file, 'r') as dest_f:
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24 data_array = numpy.genfromtxt(dest_f, skip_header=0, delimiter=delim, comments='#', dtype='string')
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25 return(data_array)
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27 def make_argparser():
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28 parser = argparse.ArgumentParser(description='Family Size Distribution of tags which were aligned to regions of the reference genome')
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29 parser.add_argument('--inputFile',
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30 help='Tabular File with three columns: ab or ba, tag and family size.')
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31 parser.add_argument('--inputName1')
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32 parser.add_argument('--ref_genome',
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33 help='TXT File with tags of reads that overlap the region.')
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34 parser.add_argument('--output_csv', default="data.csv", type=str,
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35 help='Name of the pdf and csv file.')
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36 parser.add_argument('--output_pdf', default="data.pdf", type=str,
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37 help='Name of the pdf and csv file.')
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38 parser.add_argument('--sep', default=",",
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39 help='Separator in the csv file.')
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40 return parser
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42 def compare_read_families_refGenome(argv):
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43 parser = make_argparser()
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44 args = parser.parse_args(argv[1:])
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46 firstFile = args.inputFile
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47 name1 = args.inputName1
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48 name1 = name1.split(".tabular")[0]
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49 refGenome = args.ref_genome
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50 title_file = args.output_pdf
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51 title_file2 = args.output_csv
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52 sep = args.sep
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54 if type(sep) is not str or len(sep) > 1:
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55 print("Error: --sep must be a single character.")
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56 exit(3)
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58 with open(title_file2, "w") as output_file, PdfPages(title_file) as pdf:
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59 data_array = readFileReferenceFree(firstFile, "\t")
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61 mut_array = readFileReferenceFree(refGenome, " ")
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62 length_regions = len(mut_array)
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64 seq = numpy.array(data_array[:, 1])
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65 tags = numpy.array(data_array[:, 2])
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66 quant = numpy.array(data_array[:, 0]).astype(int)
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67 group = numpy.array(mut_array[:, 0])
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69 all_ab = seq[numpy.where(tags == "ab")[0]]
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70 all_ba = seq[numpy.where(tags == "ba")[0]]
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71 quant_ab = quant[numpy.where(tags == "ab")[0]]
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72 quant_ba = quant[numpy.where(tags == "ba")[0]]
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74 seqDic_ab = dict(zip(all_ab, quant_ab))
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75 seqDic_ba = dict(zip(all_ba, quant_ba))
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77 seq_mut = numpy.array(mut_array[:, 1])
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79 groupUnique, group_index = numpy.unique(group, return_index=True)
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80 groupUnique = groupUnique[numpy.argsort(group_index)]
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82 lst_ab = []
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83 for i in seq_mut:
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84 lst_ab.append(seqDic_ab.get(i))
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86 lst_ba = []
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87 for i in seq_mut:
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88 lst_ba.append(seqDic_ba.get(i))
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89
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90 quant_ab = numpy.array(lst_ab)
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91 quant_ba = numpy.array(lst_ba)
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92
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93 quantAfterRegion = []
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94 for i in groupUnique:
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95 dataAB = quant_ab[numpy.where(group == i)[0]]
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96 dataBA = quant_ba[numpy.where(group == i)[0]]
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97 bigFamilies = numpy.where(dataAB > 20)[0]
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98 dataAB[bigFamilies] = 22
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99 bigFamilies = numpy.where(dataBA > 20)[0]
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100 dataBA[bigFamilies] = 22
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101
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102 quantAll = numpy.concatenate((dataAB, dataBA))
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103 quantAfterRegion.append(quantAll)
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104
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105 maximumX = numpy.amax(numpy.concatenate(quantAfterRegion))
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106 minimumX = numpy.amin(numpy.concatenate(quantAfterRegion))
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107
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108 ### PLOT ###
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109 plt.rc('figure', figsize=(11.69, 8.27)) # A4 format
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110 plt.rcParams['axes.facecolor'] = "E0E0E0" # grey background color
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111 plt.rcParams['xtick.labelsize'] = 12
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112 plt.rcParams['ytick.labelsize'] = 12
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113 plt.rcParams['patch.edgecolor'] = "black"
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114 fig = plt.figure()
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115 plt.subplots_adjust(bottom=0.3)
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116
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117 colors = ["#6E6E6E", "#0431B4", "#5FB404", "#B40431", "#F4FA58", "#DF7401", "#81DAF5"]
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118
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119 col = []
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120 for i in range(0, len(groupUnique)):
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121 col.append(colors[i])
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122
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123 counts = plt.hist(quantAfterRegion, bins=range(minimumX, maximumX + 1), stacked=False, label=groupUnique,
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124 align="left", alpha=1, color=col, edgecolor="black", linewidth=1)
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125 ticks = numpy.arange(minimumX - 1, maximumX, 1)
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126
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127 ticks1 = map(str, ticks)
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128 ticks1[len(ticks1) - 1] = ">20"
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129 plt.xticks(numpy.array(ticks), ticks1)
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130 count = numpy.bincount(map(int, quant_ab)) # original counts
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131
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132 legend = "max. family size =\nabsolute frequency=\nrelative frequency=\n\ntotal nr. of reads="
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133 plt.text(0.15, 0.105, legend, size=11, transform=plt.gcf().transFigure)
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134
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135 legend = "AB\n{}\n{}\n{:.5f}\n\n{:,}" \
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136 .format(max(map(int, quant_ab)), count[len(count) - 1], float(count[len(count) - 1]) / sum(count),
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137 sum(numpy.array(data_array[:, 0]).astype(int)))
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138 plt.text(0.35, 0.105, legend, size=11, transform=plt.gcf().transFigure)
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139
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140 count2 = numpy.bincount(map(int, quant_ba)) # original counts
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141
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142 legend = "BA\n{}\n{}\n{:.5f}" \
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143 .format(max(map(int, quant_ba)), count2[len(count2) - 1], float(count2[len(count2) - 1]) / sum(count2))
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144 plt.text(0.45, 0.15, legend, size=11, transform=plt.gcf().transFigure)
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145
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146 legend1 = "total nr. of tags="
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147 legend2 = "total numbers * \n{:,}".format(length_regions)
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148 plt.text(0.6, 0.2, legend1, size=11, transform=plt.gcf().transFigure)
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149 plt.text(0.75, 0.2, legend2, size=11, transform=plt.gcf().transFigure)
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150 legend4 = "* In the plot, both family sizes of the ab and ba strands were used.\nWhereas the total numbers indicate only the single count of the tags per region.\n"
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151 plt.text(0.1, 0.02, legend4, size=11, transform=plt.gcf().transFigure)
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152
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153 space = numpy.arange(0, len(groupUnique), 0.02)
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154 for i, s, count in zip(groupUnique, space, quantAfterRegion):
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155 plt.text(0.6, 0.05 + s, "{}=\n".format(i), size=11, transform=plt.gcf().transFigure)
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156 plt.text(0.75, 0.05 + s, "{:,}\n".format(len(count) / 2), size=11, transform=plt.gcf().transFigure)
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157
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158 plt.legend(loc='upper right', fontsize=14, bbox_to_anchor=(0.9, 1), frameon=True)
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159 plt.title(name1, fontsize=14)
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160 plt.xlabel("No. of Family Members", fontsize=12)
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161 plt.ylabel("Absolute Frequency", fontsize=12)
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162 plt.grid(b=True, which="major", color="#424242", linestyle=":")
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163 plt.margins(0.01, None)
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164
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165 # plt.savefig("{}_regions.pdf".format(title_file), bbox_inch="tight")
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166 pdf.savefig(fig, bbox_inch="tight")
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167 plt.close()
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168
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169 output_file.write("Dataset:{}{}\n".format(sep, firstFile))
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170 output_file.write("{}AB{}BA\n".format(sep, sep))
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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171 output_file.write("max. family size:{}{}{}{}\n".format(sep, max(map(int, quant_ab)), sep, max(map(int, quant_ba))))
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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172 output_file.write("absolute frequency:{}{}{}{}\n".format(sep, count[len(count) - 1], sep, count2[len(count2) - 1]))
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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173 output_file.write("relative frequency:{}{:.3f}{}{:.3f}\n\n".format(sep, float(count[len(count) - 1]) / sum(count), sep, float(count2[len(count2) - 1]) / sum(count2)))
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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174 output_file.write("total nr. of reads{}{}\n".format(sep, sum(numpy.array(data_array[:, 0]).astype(int))))
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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175 output_file.write("\n\nValues from family size distribution\n")
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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176 output_file.write("{}".format(sep))
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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177 for i in groupUnique:
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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178 output_file.write("{}{}".format(i,sep))
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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179 output_file.write("\n")
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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180 j=0
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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181 for fs in counts[1][0:len(counts[1])-1]:
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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182 if fs == 21:
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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183 fs = ">20"
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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184 else:
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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185 fs = "={}".format(fs)
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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186 output_file.write("FS{}{}".format(fs,sep))
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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187 for n in range(len(groupUnique)):
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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188 output_file.write("{}{}".format(int(counts[0][n][j]), sep))
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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189 output_file.write("\n")
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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190 j+=1
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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191 output_file.write("sum{}".format(sep))
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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192 for i in counts[0]:
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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193 output_file.write("{}{}".format(int(sum(i)), sep))
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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194 output_file.write("\n")
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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195 output_file.write("\n\nIn the plot, both family sizes of the ab and ba strands were used.\nWhereas the total numbers indicate only the single count of the tags per region.\n")
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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196 output_file.write("Region{}total nr. of tags per region\n".format(sep))
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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197 for i, count in zip(groupUnique, quantAfterRegion):
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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198 output_file.write("{}{}{}\n".format(i,sep,len(count) / 2))
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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199 output_file.write("sum of tags{}{}\n".format(sep,length_regions))
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200
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201 print("Files successfully created!")
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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202 #print("Files saved under {}.pdf and {}.csv in {}!".format(title_file, title_file, os.getcwd()))
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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203
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204 if __name__ == '__main__':
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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205 sys.exit(compare_read_families_refGenome(sys.argv))