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annotate fsd_regions.py @ 4:b202c97deabe draft

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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
author mheinzl
date Mon, 08 Oct 2018 05:53:50 -0400
parents 2631864873d7
children 52454637bc45
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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 tabular 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 --output_tabular outptufile_name_tabular --output_pdf outptufile_name_pdf
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15 import argparse
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16 import sys
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18 import matplotlib.pyplot as plt
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19 import numpy
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20 from matplotlib.backends.backend_pdf import PdfPages
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22 plt.switch_backend('agg')
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25 def readFileReferenceFree(file, delim):
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26 with open(file, 'r') as dest_f:
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27 data_array = numpy.genfromtxt(dest_f, skip_header=0, delimiter=delim, comments='#', dtype='string')
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28 return(data_array)
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31 def make_argparser():
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32 parser = argparse.ArgumentParser(description='Family Size Distribution of tags which were aligned to regions of the reference genome')
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33 parser.add_argument('--inputFile', help='Tabular File with three columns: ab or ba, tag and family size.')
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34 parser.add_argument('--inputName1')
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35 parser.add_argument('--ref_genome', help='TXT File with tags of reads that overlap the region.')
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36 parser.add_argument('--output_pdf', default="data.pdf", type=str, help='Name of the pdf and tabular file.')
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37 parser.add_argument('--output_tabular', default="data.tabular", type=str, help='Name of the pdf and tabular file.')
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38 return parser
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41 def compare_read_families_refGenome(argv):
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42 parser = make_argparser()
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43 args = parser.parse_args(argv[1:])
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45 firstFile = args.inputFile
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46 name1 = args.inputName1
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47 name1 = name1.split(".tabular")[0]
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48 refGenome = args.ref_genome
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49 title_file = args.output_pdf
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50 title_file2 = args.output_tabular
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51 sep = "\t"
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53 with open(title_file2, "w") as output_file, PdfPages(title_file) as pdf:
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54 data_array = readFileReferenceFree(firstFile, "\t")
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56 mut_array = readFileReferenceFree(refGenome, " ")
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57 length_regions = len(mut_array)
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59 seq = numpy.array(data_array[:, 1])
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60 tags = numpy.array(data_array[:, 2])
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61 quant = numpy.array(data_array[:, 0]).astype(int)
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62 group = numpy.array(mut_array[:, 0])
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64 all_ab = seq[numpy.where(tags == "ab")[0]]
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65 all_ba = seq[numpy.where(tags == "ba")[0]]
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66 quant_ab = quant[numpy.where(tags == "ab")[0]]
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67 quant_ba = quant[numpy.where(tags == "ba")[0]]
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69 seqDic_ab = dict(zip(all_ab, quant_ab))
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70 seqDic_ba = dict(zip(all_ba, quant_ba))
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72 seq_mut = numpy.array(mut_array[:, 1])
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74 groupUnique, group_index = numpy.unique(group, return_index=True)
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75 groupUnique = groupUnique[numpy.argsort(group_index)]
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77 lst_ab = []
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78 for i in seq_mut:
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79 lst_ab.append(seqDic_ab.get(i))
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81 lst_ba = []
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82 for i in seq_mut:
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83 lst_ba.append(seqDic_ba.get(i))
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85 quant_ab = numpy.array(lst_ab)
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86 quant_ba = numpy.array(lst_ba)
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87
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88 quantAfterRegion = []
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89 for i in groupUnique:
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90 dataAB = quant_ab[numpy.where(group == i)[0]]
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91 dataBA = quant_ba[numpy.where(group == i)[0]]
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92 bigFamilies = numpy.where(dataAB > 20)[0]
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93 dataAB[bigFamilies] = 22
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94 bigFamilies = numpy.where(dataBA > 20)[0]
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95 dataBA[bigFamilies] = 22
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96
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97 quantAll = numpy.concatenate((dataAB, dataBA))
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98 quantAfterRegion.append(quantAll)
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99
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100 maximumX = numpy.amax(numpy.concatenate(quantAfterRegion))
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101 minimumX = numpy.amin(numpy.concatenate(quantAfterRegion))
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102
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103 # PLOT
0
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104 plt.rc('figure', figsize=(11.69, 8.27)) # A4 format
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105 plt.rcParams['axes.facecolor'] = "E0E0E0" # grey background color
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106 plt.rcParams['xtick.labelsize'] = 14
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107 plt.rcParams['ytick.labelsize'] = 14
0
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108 plt.rcParams['patch.edgecolor'] = "black"
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109 fig = plt.figure()
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110 plt.subplots_adjust(bottom=0.3)
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111
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112 colors = ["#6E6E6E", "#0431B4", "#5FB404", "#B40431", "#F4FA58", "#DF7401", "#81DAF5"]
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113
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114 col = []
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115 for i in range(0, len(groupUnique)):
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116 col.append(colors[i])
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117
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118 counts = plt.hist(quantAfterRegion, bins=range(minimumX, maximumX + 1), stacked=False, label=groupUnique,
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119 align="left", alpha=1, color=col, edgecolor="black", linewidth=1)
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120 ticks = numpy.arange(minimumX - 1, maximumX, 1)
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121
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122 ticks1 = map(str, ticks)
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123 ticks1[len(ticks1) - 1] = ">20"
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124 plt.xticks(numpy.array(ticks), ticks1)
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125 count = numpy.bincount(map(int, quant_ab)) # original counts
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126
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127 legend = "max. family size =\nabsolute frequency=\nrelative frequency=\n\ntotal nr. of reads="
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128 plt.text(0.15, 0.105, legend, size=11, transform=plt.gcf().transFigure)
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129
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130 legend = "AB\n{}\n{}\n{:.5f}\n\n{:,}" \
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131 .format(max(map(int, quant_ab)), count[len(count) - 1], float(count[len(count) - 1]) / sum(count),
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132 sum(numpy.array(data_array[:, 0]).astype(int)))
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133 plt.text(0.35, 0.105, legend, size=11, transform=plt.gcf().transFigure)
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134
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135 count2 = numpy.bincount(map(int, quant_ba)) # original counts
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136
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137 legend = "BA\n{}\n{}\n{:.5f}" \
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138 .format(max(map(int, quant_ba)), count2[len(count2) - 1], float(count2[len(count2) - 1]) / sum(count2))
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139 plt.text(0.45, 0.15, legend, size=11, transform=plt.gcf().transFigure)
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140
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141 legend1 = "total nr. of tags="
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142 legend2 = "total numbers * \n{:,}".format(length_regions)
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143 plt.text(0.6, 0.2, legend1, size=11, transform=plt.gcf().transFigure)
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144 plt.text(0.75, 0.2, legend2, size=11, transform=plt.gcf().transFigure)
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145 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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146 plt.text(0.1, 0.02, legend4, size=11, transform=plt.gcf().transFigure)
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147
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148 space = numpy.arange(0, len(groupUnique), 0.02)
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149 for i, s, count in zip(groupUnique, space, quantAfterRegion):
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150 plt.text(0.6, 0.05 + s, "{}=\n".format(i), size=11, transform=plt.gcf().transFigure)
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151 plt.text(0.75, 0.05 + s, "{:,}\n".format(len(count) / 2), size=11, transform=plt.gcf().transFigure)
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152
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153 plt.legend(loc='upper right', fontsize=14, bbox_to_anchor=(0.9, 1), frameon=True)
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154 # plt.title(name1, fontsize=14)
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155 plt.xlabel("Family size", fontsize=14)
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156 plt.ylabel("Absolute Frequency", fontsize=14)
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157 plt.grid(b=True, which="major", color="#424242", linestyle=":")
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158 plt.margins(0.01, None)
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159
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160 # plt.savefig("{}_regions.pdf".format(title_file), bbox_inch="tight")
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161 pdf.savefig(fig, bbox_inch="tight")
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162 plt.close()
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163
1
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164 output_file.write("Dataset:{}{}\n".format(sep, name1))
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165 output_file.write("{}AB{}BA\n".format(sep, sep))
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166 output_file.write("max. family size:{}{}{}{}\n".format(sep, max(map(int, quant_ab)), sep, max(map(int, quant_ba))))
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167 output_file.write("absolute frequency:{}{}{}{}\n".format(sep, count[len(count) - 1], sep, count2[len(count2) - 1]))
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168 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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169 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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170 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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171 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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172 for i in groupUnique:
4
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173 output_file.write("{}{}".format(i, sep))
0
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("\n")
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175 j = 0
b202c97deabe planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
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176 for fs in counts[1][0:len(counts[1]) - 1]:
0
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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177 if fs == 21:
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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178 fs = ">20"
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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179 else:
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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180 fs = "={}".format(fs)
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181 output_file.write("FS{}{}".format(fs, sep))
0
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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182 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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183 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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184 output_file.write("\n")
4
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185 j += 1
0
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("sum{}".format(sep))
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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187 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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188 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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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 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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191 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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192 for i, count in zip(groupUnique, quantAfterRegion):
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193 output_file.write("{}{}{}\n".format(i, sep, len(count) / 2))
b202c97deabe planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
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194 output_file.write("sum of tags{}{}\n".format(sep, length_regions))
0
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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195
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196 print("Files successfully created!")
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197 # print("Files saved under {}.pdf and {}.csv in {}!".format(title_file, title_file, os.getcwd()))
b202c97deabe planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
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198
0
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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199
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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200 if __name__ == '__main__':
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201 sys.exit(compare_read_families_refGenome(sys.argv))