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annotate fsd_beforevsafter.py @ 11:fca9b000b8d8 draft

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author mheinzl
date Mon, 26 Nov 2018 04:38:21 -0500
parents 238a71241876
children
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1 #!/usr/bin/env python
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2 # Family size distribution of DCS from various steps of the Galaxy pipeline
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3 #
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4 # Author: Monika Heinzl & Gundula Povysil, Johannes-Kepler University Linz (Austria)
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5 # Contact: monika.heinzl@edumail.at
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6 #
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7 # Takes a TXT file with tags of reads that were aligned to certain regions of the reference genome (optional),
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8 # a TABULAR file with tags before the alignment to the SSCS, a FASTA file with reads that were part of the DCS and
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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9 # a FASTA file with tags after trimming as input (optional).
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10 # The program produces a plot which shows the distribution of family sizes of the DCS from the input files and
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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11 # a CSV file with the data of the plot.
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12 # USAGE: python FSD before vs after_no_refF1.3_FINAL.py --inputFile_SSCS filenameSSCS --inputName1 filenameSSCS --makeDCS filenameMakeDCS --afterTrimming filenameAfterTrimming --alignedTags DCSbamFile
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13 # --output_tabular outputfile_name_tabular --output_pdf outputfile_name_pdf
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15 import argparse
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16 import re
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17 import sys
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18 from collections import Counter
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20 import matplotlib.pyplot as plt
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21 import numpy
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22 import pysam
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23 from Bio import SeqIO
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24 from matplotlib.backends.backend_pdf import PdfPages
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26 plt.switch_backend('agg')
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29 def readFileReferenceFree(file, delim):
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30 with open(file, 'r') as dest_f:
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31 data_array = numpy.genfromtxt(dest_f, skip_header=0, delimiter=delim, comments='#', dtype='string')
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32 return(data_array)
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35 def readFasta(file):
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36 tag_consensus = []
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37 fs_consensus = []
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38 with open(file, "r") as consFile:
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39 for record in SeqIO.parse(consFile, "fasta"):
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40 tag_consensus.append(record.id)
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41 line = record.description
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42 a, b = line.split(" ")
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43 fs1, fs2 = b.split("-")
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44 fs_consensus.extend([fs1, fs2])
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45 fs_consensus = numpy.array(fs_consensus).astype(int)
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46 return(tag_consensus, fs_consensus)
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47
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48
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49 def make_argparser():
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50 parser = argparse.ArgumentParser(description='Analysis of read loss in duplex sequencing data')
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51 parser.add_argument('--inputFile_SSCS',
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52 help='Tabular File with three columns: ab or ba, tag and family size.')
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53 parser.add_argument('--inputName1')
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54 parser.add_argument('--makeDCS',
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55 help='FASTA File with information about tag and family size in the header.')
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56 parser.add_argument('--afterTrimming', default=None,
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57 help='FASTA File with information about tag and family size in the header.')
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58 parser.add_argument('--bamFile',
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59 help='BAM file with aligned reads.')
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60 parser.add_argument('--output_pdf', default="data.pdf", type=str,
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61 help='Name of the pdf and tabular file.')
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62 parser.add_argument('--output_tabular', default="data.tabular", type=str,
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63 help='Name of the pdf and tabular file.')
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64 return parser
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65
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66
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67 def compare_read_families_read_loss(argv):
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68 parser = make_argparser()
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69 args = parser.parse_args(argv[1:])
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70 #
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71 SSCS_file = args.inputFile_SSCS
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72 SSCS_file_name = args.inputName1
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73 makeConsensus = args.makeDCS
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74 afterTrimming = args.afterTrimming
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75 ref_genome = args.bamFile
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76 title_file = args.output_tabular
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77 title_file2 = args.output_pdf
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78 sep = "\t"
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80 with open(title_file, "w") as output_file, PdfPages(title_file2) as pdf:
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81 # PLOT
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82 plt.rc('figure', figsize=(11.69, 8.27)) # A4 format
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83 plt.rcParams['axes.facecolor'] = "E0E0E0" # grey background color
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84 plt.rcParams['xtick.labelsize'] = 14
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85 plt.rcParams['ytick.labelsize'] = 14
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86 plt.rcParams['patch.edgecolor'] = "black"
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87 fig = plt.figure()
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88 plt.subplots_adjust(bottom=0.3)
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89
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90 list1 = []
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91 colors = []
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92 labels = []
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93
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94 # data with tags of SSCS
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95 data_array = readFileReferenceFree(SSCS_file, "\t")
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96 seq = numpy.array(data_array[:, 1])
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97 tags = numpy.array(data_array[:, 2])
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98 quant = numpy.array(data_array[:, 0]).astype(int)
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99
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100 # split data with all tags of SSCS after ab and ba strands
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101 all_ab = seq[numpy.where(tags == "ab")[0]]
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102 all_ba = seq[numpy.where(tags == "ba")[0]]
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103 quant_ab_sscs = quant[numpy.where(tags == "ab")[0]]
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104 quant_ba_sscs = quant[numpy.where(tags == "ba")[0]]
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105
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106 seqDic_ab = dict(zip(all_ab, quant_ab_sscs))
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107 seqDic_ba = dict(zip(all_ba, quant_ba_sscs))
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108
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109 # get tags of the SSCS which form a DCS
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110 # group large family sizes
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111 bigFamilies = numpy.where(quant > 20)[0]
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112 quant[bigFamilies] = 22
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113 maximumX = numpy.amax(quant)
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114
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115 # find all unique tags and get the indices for ALL tags (ab AND ba)
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116 u, index_unique, c = numpy.unique(numpy.array(seq), return_counts=True, return_index=True)
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117 d = u[c > 1]
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118
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119 # get family sizes, tag for the duplicates
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120 duplTags_double = quant[numpy.in1d(seq, d)]
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121 list1.append(duplTags_double)
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122 colors.append("#0000FF")
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123 labels.append("before SSCS building")
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124
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125 duplTags = duplTags_double[0::2] # ab of DCS
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126 duplTagsBA = duplTags_double[1::2] # ba of DCS
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127
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128 d2 = d[(duplTags >= 3) & (duplTagsBA >= 3)] # ab and ba FS>=3
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129
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130 # all SSCSs FS>=3
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131 seq_unique, seqUnique_index = numpy.unique(seq, return_index=True)
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132 seq_unique_FS = quant[seqUnique_index]
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133 seq_unique_FS3 = seq_unique_FS[seq_unique_FS >= 3]
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134
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135 legend1 = "\ntotal nr. of tags (unique, FS>=1):\nDCS (before SSCS building, FS>=1):\ntotal nr. of tags (unique, FS>=3):\nDCS (before SSCS building, FS>=3):"
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6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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136 legend2 = "total numbers * \n{:,}\n{:,}\n{:,}\n{:,}".format(len(seq_unique_FS), len(duplTags),
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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137 len(seq_unique_FS3), len(d2))
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138 plt.text(0.55, 0.14, legend1, size=11, transform=plt.gcf().transFigure)
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139 plt.text(0.88, 0.14, legend2, size=11, transform=plt.gcf().transFigure)
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140
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141 # data make DCS
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142 tag_consensus, fs_consensus = readFasta(makeConsensus)
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143 # group large family sizes in the plot of fasta files
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144 bigFamilies = numpy.where(fs_consensus > 20)[0]
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145 fs_consensus[bigFamilies] = 22
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146 list1.append(fs_consensus)
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147 colors.append("#298A08")
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148 labels.append("after DCS building")
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149 legend3 = "after DCS building:"
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150 legend4 = "{:,}".format(len(tag_consensus))
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151 plt.text(0.55, 0.11, legend3, size=11, transform=plt.gcf().transFigure)
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152 plt.text(0.88, 0.11, legend4, size=11, transform=plt.gcf().transFigure)
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153
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154 # data after trimming
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155 if afterTrimming != str(None):
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156 tag_trimming, fs_trimming = readFasta(afterTrimming)
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157 bigFamilies = numpy.where(fs_trimming > 20)[0]
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158 fs_trimming[bigFamilies] = 22
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159 list1.append(fs_trimming)
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160 colors.append("#DF0101")
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161 labels.append("after trimming")
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162 legend5 = "after trimming:"
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163 legend6 = "{:,}".format(len(tag_trimming))
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164 plt.text(0.55, 0.09, legend5, size=11, transform=plt.gcf().transFigure)
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165 plt.text(0.88, 0.09, legend6, size=11, transform=plt.gcf().transFigure)
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166
8
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167 # data of tags aligned to reference genome
0
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168 if ref_genome != str(None):
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169 pysam.index(ref_genome)
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170 bam = pysam.AlignmentFile(ref_genome, "rb")
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171 seq_mut = []
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172 for read in bam.fetch():
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173 if not read.is_unmapped:
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174 if re.search('_', read.query_name):
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175 tags = re.split('_', read.query_name)[0]
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176 else:
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177 tags = read.query_name
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178 seq_mut.append(tags)
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179
8
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180 # use only unique tags that were alignment to the reference genome
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181 seq_mut = numpy.array(seq_mut)
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182 seq_mut, seqMut_index = numpy.unique(seq_mut, return_index=True)
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183 # get family sizes for each tag in the BAM file
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184 quant_ab = []
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185 quant_ba = []
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186 for i in seq_mut:
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187 quant_ab.append(seqDic_ab.get(i))
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188 quant_ba.append(seqDic_ba.get(i))
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189
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190 quant_ab_ref = numpy.array(quant_ab)
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191 quant_ba_ref = numpy.array(quant_ba)
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192 quant_all_ref = numpy.concatenate((quant_ab_ref, quant_ba_ref))
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193 bigFamilies = numpy.where(quant_all_ref > 20)[0] # group large family sizes
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194 quant_all_ref[bigFamilies] = 22
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195
0
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196 list1.append(quant_all_ref)
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197 colors.append("#04cec7")
5
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198 labels.append("after alignment\nto reference")
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199 legend7 = "after alignment to reference:"
0
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200 length_DCS_ref = len(quant_ba_ref) # count of duplex tags that were aligned to reference genome
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201 legend8 = "{:,}".format(length_DCS_ref)
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202 plt.text(0.55, 0.07, legend7, size=11, transform=plt.gcf().transFigure)
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203 plt.text(0.88, 0.07, legend8, size=11, transform=plt.gcf().transFigure)
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204
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205 counts = plt.hist(list1, bins=range(-1, maximumX + 1), stacked=False, label=labels, color=colors,
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206 align="left", alpha=1, edgecolor="black", linewidth=1)
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207 ticks = numpy.arange(0, maximumX, 1)
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208 ticks1 = map(str, ticks)
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209 ticks1[len(ticks1) - 1] = ">20"
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210 plt.xticks(numpy.array(ticks), ticks1)
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211 if ref_genome != str(None):
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212 count = numpy.array([v for k, v in sorted(Counter(quant_ab_ref).iteritems())]) # count all family sizes from all ab strands
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213
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214 legend = "max. family size:\nabsolute frequency:\nrelative frequency:\n\ntotal nr. of reads:\n(before SSCS building)"
fca9b000b8d8 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_beforevsafter commit 82b53a26581a2296ad272bbba1e80934864dfa58
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215 plt.text(0.1, 0.085, legend, size=11, transform=plt.gcf().transFigure)
0
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216
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217 legend = "AB\n{}\n{}\n{:.5f}\n\n{:,}" \
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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218 .format(max(quant_ab_ref), count[len(count) - 1], float(count[len(count) - 1]) / sum(count),
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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219 sum(numpy.array(data_array[:, 0]).astype(int)))
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220 plt.text(0.35, 0.105, legend, size=11, transform=plt.gcf().transFigure)
0
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221
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222 count2 = numpy.array(
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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223 [v for k, v in sorted(Counter(quant_ba_ref).iteritems())]) # count all family sizes from all ba strands
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224 legend = "BA\n{}\n{}\n{:.5f}" \
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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225 .format(max(quant_ba_ref), count2[len(count2) - 1], float(count2[len(count2) - 1]) / sum(count2))
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226 plt.text(0.45, 0.1475, legend, size=11, transform=plt.gcf().transFigure)
0
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227
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228 legend4 = "* In the plot, the family sizes of ab and ba strands and of both duplex tags were used.\nWhereas the total numbers indicate only the single count of the formed duplex tags."
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229 plt.text(0.1, 0.02, legend4, size=11, transform=plt.gcf().transFigure)
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230
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231 plt.legend(loc='upper right', fontsize=14, bbox_to_anchor=(0.9, 1), frameon=True)
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232 plt.title("Family size distribution of tags from various steps of the Du Novo pipeline", fontsize=14)
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233 plt.xlabel("Family size", fontsize=14)
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234 plt.ylabel("Absolute Frequency", fontsize=14)
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235 plt.grid(b=True, which="major", color="#424242", linestyle=":")
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236 plt.margins(0.01, None)
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237
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238 pdf.savefig(fig, bbox_inch="tight")
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239 plt.close()
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
240
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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241 # write information about plot into a csv file
2
e8115b71edbd planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit b9403b3ce2b7a41fa8ee1aa47909152de78cf641
mheinzl
parents: 0
diff changeset
242 output_file.write("Dataset:{}{}\n".format(sep, SSCS_file_name))
0
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
243 if ref_genome != str(None):
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
244 output_file.write("{}AB{}BA\n".format(sep, sep))
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
245 output_file.write("max. family size:{}{}{}{}\n".format(sep, max(quant_ab_ref), sep, max(quant_ba_ref)))
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
246 output_file.write(
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
247 "absolute frequency:{}{}{}{}\n".format(sep, count[len(count) - 1], sep, count2[len(count2) - 1]))
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
248 output_file.write(
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
249 "relative frequency:{}{:.3f}{}{:.3f}\n\n".format(sep, float(count[len(count) - 1]) / sum(count), sep,
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
250 float(count2[len(count2) - 1]) / sum(count2)))
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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251
11
fca9b000b8d8 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_beforevsafter commit 82b53a26581a2296ad272bbba1e80934864dfa58
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diff changeset
252 output_file.write("\ntotal nr. of reads before SSCS building{}{}\n".format(sep, sum(numpy.array(data_array[:, 0]).astype(int))))
0
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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diff changeset
253 output_file.write("\n\nValues from family size distribution\n")
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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254
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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255 if afterTrimming == str(None) and ref_genome == str(None):
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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256 if afterTrimming == str(None):
11
fca9b000b8d8 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_beforevsafter commit 82b53a26581a2296ad272bbba1e80934864dfa58
mheinzl
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diff changeset
257 output_file.write("{}before SSCS building{}after DCS building\n".format(sep, sep))
0
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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258 elif ref_genome == str(None):
8
238a71241876 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_beforevsafter commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
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diff changeset
259 output_file.write("{}before SSCS building{}atfer DCS building\n".format(sep, sep))
0
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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260
8
238a71241876 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_beforevsafter commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
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diff changeset
261 for fs, sscs, dcs in zip(counts[1][2:len(counts[1])], counts[0][0][2:len(counts[0][0])], counts[0][1][2:len(counts[0][1])]):
0
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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262 if fs == 21:
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
263 fs = ">20"
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
264 else:
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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265 fs = "={}".format(fs)
8
238a71241876 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_beforevsafter commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
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diff changeset
266 output_file.write("FS{}{}{}{}{}\n".format(fs, sep, int(sscs), sep, int(dcs)))
238a71241876 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_beforevsafter commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
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diff changeset
267 output_file.write("sum{}{}{}{}\n".format(sep, int(sum(counts[0][0])), sep, int(sum(counts[0][1]))))
0
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
268
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
269 elif afterTrimming == str(None) or ref_genome == str(None):
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
270 if afterTrimming == str(None):
11
fca9b000b8d8 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_beforevsafter commit 82b53a26581a2296ad272bbba1e80934864dfa58
mheinzl
parents: 8
diff changeset
271 output_file.write("{}before SSCS building{}after DCS building{}after alignment to reference\n".format(sep, sep, sep))
0
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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272 elif ref_genome == str(None):
8
238a71241876 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_beforevsafter commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
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diff changeset
273 output_file.write("{}before SSCS building{}atfer DCS building{}after trimming\n".format(sep, sep, sep))
0
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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274
8
238a71241876 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_beforevsafter commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
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diff changeset
275 for fs, sscs, dcs, reference in zip(counts[1][2:len(counts[1])], counts[0][0][2:len(counts[0][0])], counts[0][1][2:len(counts[0][1])], counts[0][2][2:len(counts[0][2])]):
0
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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276 if fs == 21:
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
277 fs = ">20"
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
278 else:
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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diff changeset
279 fs = "={}".format(fs)
8
238a71241876 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_beforevsafter commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
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diff changeset
280 output_file.write("FS{}{}{}{}{}{}{}\n".format(fs, sep, int(sscs), sep, int(dcs), sep, int(reference)))
238a71241876 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_beforevsafter commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
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diff changeset
281 output_file.write("sum{}{}{}{}{}{}\n".format(sep, int(sum(counts[0][0])), sep, int(sum(counts[0][1])), sep, int(sum(counts[0][2]))))
0
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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diff changeset
282
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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diff changeset
283 else:
8
238a71241876 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_beforevsafter commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
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diff changeset
284 output_file.write("{}before SSCS building{}after DCS building{}after trimming{}after alignment to reference\n".format(sep, sep, sep, sep))
238a71241876 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_beforevsafter commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
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diff changeset
285 for fs, sscs, dcs, trim, reference in zip(counts[1][2:len(counts[1])], counts[0][0][2:len(counts[0][0])], counts[0][1][2:len(counts[0][1])], counts[0][2][2:len(counts[0][2])], counts[0][3][2:len(counts[0][3])]):
0
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
286 if fs == 21:
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
287 fs = ">20"
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
288 else:
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
289 fs = "={}".format(fs)
8
238a71241876 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_beforevsafter commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
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diff changeset
290 output_file.write("FS{}{}{}{}{}{}{}{}{}\n".format(fs, sep, int(sscs), sep, int(dcs), sep, int(trim), sep, int(reference)))
238a71241876 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_beforevsafter commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
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diff changeset
291 output_file.write("sum{}{}{}{}{}{}{}{}\n".format(sep, int(sum(counts[0][0])), sep, int(sum(counts[0][1])), sep, int(sum(counts[0][2])), sep, int(sum(counts[0][3]))))
0
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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diff changeset
292
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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diff changeset
293 output_file.write("\n\nIn the plot, the family sizes of ab and ba strands and of both duplex tags were used.\nWhereas the total numbers indicate only the single count of the formed duplex tags.\n")
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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diff changeset
294 output_file.write("total nr. of tags (unique, FS>=1){}{}\n".format(sep, len(seq_unique_FS)))
5
1eae0524b285 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit f4eb0a7cd4fd5baaa9afe0c931afb57ac6abc0c1
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parents: 3
diff changeset
295 output_file.write("DCS (before SSCS building, FS>=1){}{}\n".format(sep, len(duplTags)))
0
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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diff changeset
296 output_file.write("total nr. of tags (unique, FS>=3){}{}\n".format(sep, len(seq_unique_FS3)))
5
1eae0524b285 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit f4eb0a7cd4fd5baaa9afe0c931afb57ac6abc0c1
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diff changeset
297 output_file.write("DCS (before SSCS building, FS>=3){}{}\n".format(sep, len(d2)))
1eae0524b285 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit f4eb0a7cd4fd5baaa9afe0c931afb57ac6abc0c1
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diff changeset
298 output_file.write("after DCS building{}{}\n".format(sep, len(tag_consensus)))
0
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
299 if afterTrimming != str(None):
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
300 output_file.write("after trimming{}{}\n".format(sep, len(tag_trimming)))
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
301 if ref_genome != str(None):
5
1eae0524b285 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit f4eb0a7cd4fd5baaa9afe0c931afb57ac6abc0c1
mheinzl
parents: 3
diff changeset
302 output_file.write("after alignment to reference{}{}\n".format(sep, length_DCS_ref))
0
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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diff changeset
303
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
304 print("Files successfully created!")
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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diff changeset
305
8
238a71241876 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_beforevsafter commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 5
diff changeset
306
0
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
307 if __name__ == '__main__':
8
238a71241876 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_beforevsafter commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
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diff changeset
308 sys.exit(compare_read_families_read_loss(sys.argv))