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annotate fsd_beforevsafter.py @ 3:327c40a821ed draft

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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 29bc65d5627553741c83ce1f298223e2b266f7c8
author mheinzl
date Tue, 15 May 2018 14:22:10 -0400
parents e8115b71edbd
children 1eae0524b285
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1 #!/usr/bin/env python
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3 # Family size distribution of DCS from various steps of the Galaxy pipeline
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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 a TXT file with tags of reads that were aligned to certain regions of the reference genome (optional),
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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9 # 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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10 # a FASTA file with tags after trimming as input (optional).
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11 # 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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12 # a CSV file with the data of the plot.
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14 # USAGE: python FSD before vs after_no_refF1.3_FINAL.py --inputFile_SSCS filenameSSCS --inputName1 filenameSSCS --makeDCS filenameMakeDCS --afterTrimming filenameAfterTrimming -- alignedTags filenameTagsRefGenome
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15 # --sep "characterWhichSeparatesCSVFile" --output_csv outptufile_name_csv --output_pdf outptufile_name_pdf
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18 import numpy
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19 import matplotlib.pyplot as plt
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20 from collections import Counter
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21 from Bio import SeqIO
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22 import argparse
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23 import sys
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24 import os
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25 from matplotlib.backends.backend_pdf import PdfPages
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27 def readFileReferenceFree(file, delim):
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28 with open(file, 'r') as dest_f:
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29 data_array = numpy.genfromtxt(dest_f, skip_header=0, delimiter=delim, comments='#', dtype='string')
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30 return(data_array)
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32 def readFasta(file):
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33 tag_consensus = []
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34 fs_consensus = []
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35 with open(file, "r") as consFile:
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36 for record in SeqIO.parse(consFile, "fasta"):
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37 tag_consensus.append(record.id)
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38 line = record.description
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39 a, b = line.split(" ")
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40 fs1, fs2 = b.split("-")
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41 fs_consensus.extend([fs1,fs2])
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42 fs_consensus = numpy.array(fs_consensus).astype(int)
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43 return(tag_consensus, fs_consensus)
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44
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45 def make_argparser():
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46 parser = argparse.ArgumentParser(description='Analysis of read loss in duplex sequencing data')
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47 parser.add_argument('--inputFile_SSCS',
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48 help='Tabular File with three columns: ab or ba, tag and family size.')
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49 parser.add_argument('--inputName1')
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50 parser.add_argument('--makeDCS',
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51 help='FASTA File with information about tag and family size in the header.')
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52 parser.add_argument('--afterTrimming',default=None,
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53 help='FASTA File with information about tag and family size in the header.')
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54 parser.add_argument('--alignedTags',default=None,
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55 help=' TXT file with tags aligned to the reference genome and family size.')
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56 parser.add_argument('--output_pdf', default="data.pdf", type=str,
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57 help='Name of the pdf and csv file.')
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58 parser.add_argument('--output_csv', default="data.csv", type=str,
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59 help='Name of the pdf and csv file.')
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60 parser.add_argument('--sep', default=",",
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61 help='Separator in the csv file.')
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62 return parser
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63
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64 def compare_read_families_read_loss(argv):
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65 parser = make_argparser()
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66 args = parser.parse_args(argv[1:])
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67
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68 SSCS_file = args.inputFile_SSCS
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69 SSCS_file_name = args.inputName1
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70 makeConsensus = args.makeDCS
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71 afterTrimming = args.afterTrimming
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72 ref_genome = args.alignedTags
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73 title_file = args.output_csv
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74 title_file2 = args.output_pdf
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75 sep = args.sep
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76
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77 if type(sep) is not str or len(sep)>1:
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78 print("Error: --sep must be a single character.")
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79 exit(4)
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80
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81 with open(title_file, "w") as output_file, PdfPages(title_file2) as pdf:
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82 ### PLOT ###
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83 plt.rc('figure', figsize=(11.69, 8.27)) # A4 format
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84 plt.rcParams['axes.facecolor'] = "E0E0E0" # grey background color
2
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85 plt.rcParams['xtick.labelsize'] = 14
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86 plt.rcParams['ytick.labelsize'] = 14
0
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87 plt.rcParams['patch.edgecolor'] = "black"
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88 fig = plt.figure()
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89 plt.subplots_adjust(bottom=0.3)
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90
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91 list1 = []
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92 colors = []
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93 labels = []
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94
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95 ### data with tags of SSCS
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96 data_array = readFileReferenceFree(SSCS_file, "\t")
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97 seq = numpy.array(data_array[:, 1])
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98 tags = numpy.array(data_array[:, 2])
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99 quant = numpy.array(data_array[:, 0]).astype(int)
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100
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101 # split data with all tags of SSCS after ab and ba strands
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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102 all_ab = seq[numpy.where(tags == "ab")[0]]
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103 all_ba = seq[numpy.where(tags == "ba")[0]]
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104 quant_ab_sscs = quant[numpy.where(tags == "ab")[0]]
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105 quant_ba_sscs = quant[numpy.where(tags == "ba")[0]]
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106
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107 seqDic_ab = dict(zip(all_ab, quant_ab_sscs))
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108 seqDic_ba = dict(zip(all_ba, quant_ba_sscs))
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109
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110 ### get tags of the SSCS which form a DCS
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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111 # group large family sizes
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112 bigFamilies = numpy.where(quant > 20)[0]
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113 quant[bigFamilies] = 22
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114 maximumX = numpy.amax(quant)
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115
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116 # find all unique tags and get the indices for ALL tags (ab AND ba)
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117 u, index_unique, c = numpy.unique(numpy.array(seq), return_counts=True, return_index=True)
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118 d = u[c > 1]
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119
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120 # get family sizes, tag for the duplicates
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121 duplTags_double = quant[numpy.in1d(seq, d)]
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122 list1.append(duplTags_double)
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123 colors.append("#0000FF")
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124 labels.append("before alignment\nto SSCS")
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125
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126 duplTags = duplTags_double[0::2] # ab of DCS
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127 duplTagsBA = duplTags_double[1::2] # ba of DCS
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128
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129 d2 = d[(duplTags >= 3) & (duplTagsBA >= 3)] # ab and ba FS>=3
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130
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131 # all SSCSs FS>=3
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132 seq_unique, seqUnique_index = numpy.unique(seq, return_index=True)
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133 seq_unique_FS = quant[seqUnique_index]
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134 seq_unique_FS3 = seq_unique_FS[seq_unique_FS >= 3]
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135
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136 legend1 = "\ntotal nr. of tags (unique, FS>=1):\nDCS (before alignment to SSCS, FS>=1):\ntotal nr. of tags (unique, FS>=3):\nDCS (before alignment to SSCS, FS>=3):"
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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137 legend2 = "total numbers * \n{:,}\n{:,}\n{:,}\n{:,}".format(len(seq_unique_FS), len(duplTags),
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138 len(seq_unique_FS3), len(d2))
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139 plt.text(0.55, 0.14, legend1, size=11, transform=plt.gcf().transFigure)
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140 plt.text(0.88, 0.14, legend2, size=11, transform=plt.gcf().transFigure)
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141
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142 ## data make DCS
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143 tag_consensus, fs_consensus = readFasta(makeConsensus)
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144 ### group large family sizes in the plot of fasta files
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145 bigFamilies = numpy.where(fs_consensus > 20)[0]
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146 fs_consensus[bigFamilies] = 22
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147 list1.append(fs_consensus)
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148 colors.append("#298A08")
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149 labels.append("make DCS")
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150 legend3 = "make DCS:"
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151 legend4 = "{:,}".format(len(tag_consensus))
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152 plt.text(0.55, 0.11, legend3, size=11, transform=plt.gcf().transFigure)
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153 plt.text(0.88, 0.11, legend4, size=11, transform=plt.gcf().transFigure)
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154
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155 ### data after trimming
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156 if afterTrimming != str(None):
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157 tag_trimming, fs_trimming = readFasta(afterTrimming)
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158 bigFamilies = numpy.where(fs_trimming > 20)[0]
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159 fs_trimming[bigFamilies] = 22
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160 list1.append(fs_trimming)
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161 colors.append("#DF0101")
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162 labels.append("after trimming")
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163 legend5 = "after trimming:"
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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164 legend6 = "{:,}".format(len(tag_trimming))
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165 plt.text(0.55, 0.09, legend5, size=11, transform=plt.gcf().transFigure)
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166 plt.text(0.88, 0.09, legend6, size=11, transform=plt.gcf().transFigure)
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167
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168 ### data of tags aligned to reference genome
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169 if ref_genome != str(None):
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170 mut_array = readFileReferenceFree(ref_genome, " ")
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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171 ### use only unique tags that were alignment to the reference genome
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172 seq_mut, seqMut_index = numpy.unique(numpy.array(mut_array[:, 1]), return_index=True)
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173
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174 # get family sizes
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175 quant_ab = []
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176 for i in seq_mut:
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177 quant_ab.append(seqDic_ab.get(i))
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178
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179 quant_ba = []
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180 for i in seq_mut:
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181 quant_ba.append(seqDic_ba.get(i))
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182
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183 quant_ab_ref = numpy.array(quant_ab)
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184 quant_ba_ref = numpy.array(quant_ba)
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185 quant_all_ref = numpy.concatenate((quant_ab_ref, quant_ba_ref))
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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186 bigFamilies = numpy.where(quant_all_ref > 20)[0] # group large family sizes
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187 quant_all_ref[bigFamilies] = 22
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188 list1.append(quant_all_ref)
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189 colors.append("#04cec7")
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190 labels.append("after alignment\nto reference genome")
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191 legend7 = "after alignment to reference genome:"
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192 length_DCS_ref = len(quant_ba_ref) # count of duplex tags that were aligned to reference genome
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193 legend8 = "{:,}".format(length_DCS_ref)
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194 plt.text(0.55, 0.07, legend7, size=11, transform=plt.gcf().transFigure)
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195 plt.text(0.88, 0.07, legend8, size=11, transform=plt.gcf().transFigure)
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196
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197
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198 counts = plt.hist(list1, bins=range(-1, maximumX + 1), stacked=False, label=labels, color=colors,
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199 align="left", alpha=1, edgecolor="black", linewidth=1)
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200 ticks = numpy.arange(0, maximumX, 1)
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201 ticks1 = map(str, ticks)
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202 ticks1[len(ticks1) - 1] = ">20"
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203 plt.xticks(numpy.array(ticks), ticks1)
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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204 if ref_genome != str(None):
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205 count = numpy.array(
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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206 [v for k, v in sorted(Counter(quant_ab_ref).iteritems())]) # count all family sizes from all ab strands
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207
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208 legend = "max. family size =\nabsolute frequency=\nrelative frequency=\n\ntotal nr. of reads (before)"
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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209 plt.text(0.1, 0.105, legend, size=11, transform=plt.gcf().transFigure)
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210
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211 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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212 .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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213 sum(numpy.array(data_array[:, 0]).astype(int)))
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214 plt.text(0.3, 0.105, legend, size=11, transform=plt.gcf().transFigure)
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215
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216 count2 = numpy.array(
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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217 [v for k, v in sorted(Counter(quant_ba_ref).iteritems())]) # count all family sizes from all ba strands
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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218 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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219 .format(max(quant_ba_ref), count2[len(count2) - 1], float(count2[len(count2) - 1]) / sum(count2))
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220 plt.text(0.4, 0.15, legend, size=11, transform=plt.gcf().transFigure)
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221
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222 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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223 plt.text(0.1, 0.02, legend4, size=11, transform=plt.gcf().transFigure)
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224
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225 plt.legend(loc='upper right', fontsize=14, bbox_to_anchor=(0.9, 1), frameon=True)
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226 plt.title("Family size distribution of tags from various steps of the Du Novo pipeline", fontsize=14)
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227 plt.xlabel("Family size", fontsize=14)
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228 plt.ylabel("Absolute Frequency", fontsize=14)
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229 plt.grid(b=True, which="major", color="#424242", linestyle=":")
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230 plt.margins(0.01, None)
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231
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232 pdf.savefig(fig, bbox_inch="tight")
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233 plt.close()
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234
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235 # write information about plot into a csv file
2
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236 output_file.write("Dataset:{}{}\n".format(sep, SSCS_file_name))
0
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237 if ref_genome != str(None):
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238 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
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239 output_file.write("max. family size:{}{}{}{}\n".format(sep, max(quant_ab_ref), sep, max(quant_ba_ref)))
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240 output_file.write(
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diff changeset
241 "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
parents:
diff changeset
242 output_file.write(
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
243 "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
parents:
diff changeset
244 float(count2[len(count2) - 1]) / sum(count2)))
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
245
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("\n\ntotal nr. of reads{}{}\n".format(sep, sum(numpy.array(data_array[:, 0]).astype(int))))
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
247 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
mheinzl
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diff changeset
248
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
249 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
mheinzl
parents:
diff changeset
250 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
251 output_file.write(
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
252 "{}before alignment to SSCS{}make DCS\n".format(sep, sep))
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
253 elif ref_genome == str(None):
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
254 output_file.write(
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
255 "{}before alignment to SSCS{}make DCS\n".format(sep, sep))
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
256
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
257 for fs, sscs, dcs in zip(counts[1][2:len(counts[1])], counts[0][0][2:len(counts[0][0])],
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
258 counts[0][1][2:len(counts[0][1])]):
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
259 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
260 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
261 else:
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
262 fs = "={}".format(fs)
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
263 output_file.write(
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
264 "FS{}{}{}{}{}\n".format(fs, sep, int(sscs), sep, int(dcs)))
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
265 output_file.write(
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
266 "sum{}{}{}{}\n".format(sep, int(sum(counts[0][0])), sep, int(sum(counts[0][1]))))
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
267
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
268 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
parents:
diff changeset
269 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
270 output_file.write(
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
271 "{}before alignment to SSCS{}make DCS{}after alignment to reference genome\n".format(sep, sep, sep))
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
272 elif ref_genome == str(None):
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
273 output_file.write(
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
274 "{}before alignment to SSCS{}make DCS{}after trimming\n".format(sep, 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
275
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
276 for fs, sscs, dcs, reference in zip(counts[1][2:len(counts[1])], counts[0][0][2:len(counts[0][0])],
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
277 counts[0][1][2:len(counts[0][1])],counts[0][2][2:len(counts[0][2])]):
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
278 if fs == 21:
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
279 fs = ">20"
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
280 else:
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
281 fs = "={}".format(fs)
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
282 output_file.write(
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
283 "FS{}{}{}{}{}{}{}\n".format(fs, sep, int(sscs), sep, int(dcs), sep, int(reference)))
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
284 output_file.write(
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
285 "sum{}{}{}{}{}{}\n".format(sep, int(sum(counts[0][0])), sep, int(sum(counts[0][1])), sep, int(sum(counts[0][2]))))
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
286
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
287 else:
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
288 output_file.write(
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
289 "{}before alignment to SSCS{}make DCS{}after trimming{}after alignment to reference genome\n".format(
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
290 sep, sep, sep, sep))
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
291 for fs, sscs, dcs, trim, reference in zip(counts[1][2:len(counts[1])], counts[0][0][2:len(counts[0][0])],
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
292 counts[0][1][2:len(counts[0][1])],
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
293 counts[0][2][2:len(counts[0][2])],
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
294 counts[0][3][2:len(counts[0][3])]):
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
295 if fs == 21:
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
296 fs = ">20"
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
297 else:
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
298 fs = "={}".format(fs)
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
299 output_file.write(
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
300 "FS{}{}{}{}{}{}{}{}{}\n".format(fs, sep, int(sscs), sep, int(dcs), sep, int(trim), sep,
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
301 int(reference)))
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
302 output_file.write(
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
303 "sum{}{}{}{}{}{}{}{}\n".format(sep, int(sum(counts[0][0])), sep, int(sum(counts[0][1])), sep,
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
304 int(sum(counts[0][2])), sep, int(sum(counts[0][3]))))
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
305
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
306 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
mheinzl
parents:
diff changeset
307 output_file.write("total nr. of tags (unique, FS>=1){}{}\n".format(sep, len(seq_unique_FS)))
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
308 output_file.write("DCS (before alignment to SSCS, FS>=1){}{}\n".format(sep, len(duplTags)))
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
309 output_file.write("total nr. of tags (unique, FS>=3){}{}\n".format(sep, len(seq_unique_FS3)))
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
310 output_file.write("DCS (before alignment to SSCS, FS>=3){}{}\n".format(sep, len(d2)))
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
311 output_file.write("make DCS{}{}\n".format(sep, len(tag_consensus)))
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
312 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
313 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
parents:
diff changeset
314 if ref_genome != str(None):
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
315 output_file.write("after alignment to reference genome{}{}\n".format(sep, length_DCS_ref))
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
316
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
317 print("Files successfully created!")
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
318
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
319 if __name__ == '__main__':
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
320 sys.exit(compare_read_families_read_loss(sys.argv))