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annotate fsd_beforevsafter.py @ 8:238a71241876 draft

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author mheinzl
date Mon, 08 Oct 2018 05:55:14 -0400
parents 1eae0524b285
children fca9b000b8d8
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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, 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
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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
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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 filenameTagsRefGenome
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13 # --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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17 from collections import Counter
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19 import matplotlib.pyplot as plt
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20 import numpy
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21 from Bio import SeqIO
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22 from matplotlib.backends.backend_pdf import PdfPages
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24 plt.switch_backend('agg')
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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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33 def readFasta(file):
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34 tag_consensus = []
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35 fs_consensus = []
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36 with open(file, "r") as consFile:
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37 for record in SeqIO.parse(consFile, "fasta"):
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38 tag_consensus.append(record.id)
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39 line = record.description
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40 a, b = line.split(" ")
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41 fs1, fs2 = b.split("-")
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42 fs_consensus.extend([fs1, fs2])
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43 fs_consensus = numpy.array(fs_consensus).astype(int)
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44 return(tag_consensus, fs_consensus)
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45
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47 def make_argparser():
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48 parser = argparse.ArgumentParser(description='Analysis of read loss in duplex sequencing data')
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49 parser.add_argument('--inputFile_SSCS',
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50 help='Tabular File with three columns: ab or ba, tag and family size.')
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51 parser.add_argument('--inputName1')
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52 parser.add_argument('--makeDCS',
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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('--afterTrimming', default=None,
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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('--alignedTags', default=None,
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57 help=' TXT file with tags aligned to the reference genome and family size.')
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58 parser.add_argument('--output_pdf', default="data.pdf", type=str,
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59 help='Name of the pdf and tabular file.')
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60 parser.add_argument('--output_tabular', default="data.tabular", type=str,
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61 help='Name of the pdf and tabular file.')
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62 return parser
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63
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64
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65 def compare_read_families_read_loss(argv):
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66 parser = make_argparser()
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67 args = parser.parse_args(argv[1:])
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68
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69 SSCS_file = args.inputFile_SSCS
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70 SSCS_file_name = args.inputName1
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71 makeConsensus = args.makeDCS
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72 afterTrimming = args.afterTrimming
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73 ref_genome = args.alignedTags
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74 title_file = args.output_tabular
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75 title_file2 = args.output_pdf
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76 sep = "\t"
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77
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78 with open(title_file, "w") as output_file, PdfPages(title_file2) as pdf:
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79 # PLOT
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80 plt.rc('figure', figsize=(11.69, 8.27)) # A4 format
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81 plt.rcParams['axes.facecolor'] = "E0E0E0" # grey background color
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82 plt.rcParams['xtick.labelsize'] = 14
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83 plt.rcParams['ytick.labelsize'] = 14
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84 plt.rcParams['patch.edgecolor'] = "black"
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85 fig = plt.figure()
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86 plt.subplots_adjust(bottom=0.3)
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87
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88 list1 = []
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89 colors = []
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90 labels = []
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91
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92 # data with tags of SSCS
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93 data_array = readFileReferenceFree(SSCS_file, "\t")
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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94 seq = numpy.array(data_array[:, 1])
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95 tags = numpy.array(data_array[:, 2])
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96 quant = numpy.array(data_array[:, 0]).astype(int)
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97
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98 # 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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99 all_ab = seq[numpy.where(tags == "ab")[0]]
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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100 all_ba = seq[numpy.where(tags == "ba")[0]]
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101 quant_ab_sscs = quant[numpy.where(tags == "ab")[0]]
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102 quant_ba_sscs = quant[numpy.where(tags == "ba")[0]]
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103
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104 seqDic_ab = dict(zip(all_ab, quant_ab_sscs))
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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105 seqDic_ba = dict(zip(all_ba, quant_ba_sscs))
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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106
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107 # get tags of the SSCS which form a DCS
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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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108 # group large family sizes
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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109 bigFamilies = numpy.where(quant > 20)[0]
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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110 quant[bigFamilies] = 22
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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111 maximumX = numpy.amax(quant)
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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112
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113 # find all unique tags and get the indices for ALL tags (ab AND ba)
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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114 u, index_unique, c = numpy.unique(numpy.array(seq), return_counts=True, return_index=True)
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115 d = u[c > 1]
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116
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117 # get family sizes, tag for the duplicates
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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118 duplTags_double = quant[numpy.in1d(seq, d)]
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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119 list1.append(duplTags_double)
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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120 colors.append("#0000FF")
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121 labels.append("before SSCS building")
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122
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123 duplTags = duplTags_double[0::2] # ab of DCS
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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124 duplTagsBA = duplTags_double[1::2] # ba of DCS
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125
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126 d2 = d[(duplTags >= 3) & (duplTagsBA >= 3)] # ab and ba FS>=3
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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127
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128 # all SSCSs FS>=3
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129 seq_unique, seqUnique_index = numpy.unique(seq, return_index=True)
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130 seq_unique_FS = quant[seqUnique_index]
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131 seq_unique_FS3 = seq_unique_FS[seq_unique_FS >= 3]
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132
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133 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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134 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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135 len(seq_unique_FS3), len(d2))
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136 plt.text(0.55, 0.14, legend1, size=11, transform=plt.gcf().transFigure)
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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137 plt.text(0.88, 0.14, legend2, size=11, transform=plt.gcf().transFigure)
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138
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139 # data make DCS
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140 tag_consensus, fs_consensus = readFasta(makeConsensus)
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141 # group large family sizes in the plot of fasta files
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142 bigFamilies = numpy.where(fs_consensus > 20)[0]
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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143 fs_consensus[bigFamilies] = 22
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144 list1.append(fs_consensus)
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145 colors.append("#298A08")
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146 labels.append("after DCS building")
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147 legend3 = "after DCS building:"
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148 legend4 = "{:,}".format(len(tag_consensus))
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149 plt.text(0.55, 0.11, legend3, size=11, transform=plt.gcf().transFigure)
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150 plt.text(0.88, 0.11, legend4, size=11, transform=plt.gcf().transFigure)
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151
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152 # data after trimming
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153 if afterTrimming != str(None):
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154 tag_trimming, fs_trimming = readFasta(afterTrimming)
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155 bigFamilies = numpy.where(fs_trimming > 20)[0]
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156 fs_trimming[bigFamilies] = 22
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157 list1.append(fs_trimming)
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158 colors.append("#DF0101")
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159 labels.append("after trimming")
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160 legend5 = "after trimming:"
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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161 legend6 = "{:,}".format(len(tag_trimming))
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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162 plt.text(0.55, 0.09, legend5, size=11, transform=plt.gcf().transFigure)
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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163 plt.text(0.88, 0.09, legend6, size=11, transform=plt.gcf().transFigure)
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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164
8
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165 # data of tags aligned to reference genome
0
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166 if ref_genome != str(None):
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167 mut_array = readFileReferenceFree(ref_genome, " ")
8
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168 # use only unique tags that were alignment to the reference genome
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169 seq_mut, seqMut_index = numpy.unique(numpy.array(mut_array[:, 1]), return_index=True)
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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170
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171 # get family sizes
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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172 quant_ab = []
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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173 for i in seq_mut:
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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174 quant_ab.append(seqDic_ab.get(i))
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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175
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176 quant_ba = []
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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177 for i in seq_mut:
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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178 quant_ba.append(seqDic_ba.get(i))
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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179
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180 quant_ab_ref = numpy.array(quant_ab)
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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181 quant_ba_ref = numpy.array(quant_ba)
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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182 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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183 bigFamilies = numpy.where(quant_all_ref > 20)[0] # group large family sizes
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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184 quant_all_ref[bigFamilies] = 22
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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185 list1.append(quant_all_ref)
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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186 colors.append("#04cec7")
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187 labels.append("after alignment\nto reference")
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188 legend7 = "after alignment to reference:"
0
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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189 length_DCS_ref = len(quant_ba_ref) # count of duplex tags that were aligned to reference genome
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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190 legend8 = "{:,}".format(length_DCS_ref)
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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191 plt.text(0.55, 0.07, legend7, size=11, transform=plt.gcf().transFigure)
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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192 plt.text(0.88, 0.07, legend8, size=11, transform=plt.gcf().transFigure)
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193
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194 counts = plt.hist(list1, bins=range(-1, maximumX + 1), stacked=False, label=labels, color=colors,
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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195 align="left", alpha=1, edgecolor="black", linewidth=1)
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196 ticks = numpy.arange(0, maximumX, 1)
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197 ticks1 = map(str, ticks)
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198 ticks1[len(ticks1) - 1] = ">20"
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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199 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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200 if ref_genome != str(None):
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201 count = numpy.array(
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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202 [v for k, v in sorted(Counter(quant_ab_ref).iteritems())]) # count all family sizes from all ab strands
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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203
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204 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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205 plt.text(0.1, 0.105, legend, size=11, transform=plt.gcf().transFigure)
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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206
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207 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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208 .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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209 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
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210 plt.text(0.3, 0.105, legend, size=11, transform=plt.gcf().transFigure)
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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211
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212 count2 = numpy.array(
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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213 [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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214 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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215 .format(max(quant_ba_ref), count2[len(count2) - 1], 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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216 plt.text(0.4, 0.15, legend, size=11, transform=plt.gcf().transFigure)
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217
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218 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."
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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219 plt.text(0.1, 0.02, legend4, size=11, transform=plt.gcf().transFigure)
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220
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221 plt.legend(loc='upper right', fontsize=14, bbox_to_anchor=(0.9, 1), frameon=True)
2
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222 plt.title("Family size distribution of tags from various steps of the Du Novo pipeline", fontsize=14)
e8115b71edbd planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit b9403b3ce2b7a41fa8ee1aa47909152de78cf641
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223 plt.xlabel("Family size", fontsize=14)
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224 plt.ylabel("Absolute Frequency", fontsize=14)
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225 plt.grid(b=True, which="major", color="#424242", linestyle=":")
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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226 plt.margins(0.01, None)
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227
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228 pdf.savefig(fig, bbox_inch="tight")
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229 plt.close()
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230
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231 # write information about plot into a csv file
2
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232 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
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233 if 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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234 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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235 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
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236 output_file.write(
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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237 "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
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238 output_file.write(
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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diff changeset
239 "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
240 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
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241
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
242 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
243 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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244
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 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
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246 if afterTrimming == 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
247 output_file.write("{}before SSCS buidling{}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
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248 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
249 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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250
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
251 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
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252 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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253 fs = ">20"
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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254 else:
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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255 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
256 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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257 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
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258
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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diff changeset
259 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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260 if afterTrimming == 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
261 output_file.write("{}before SSCS buidling{}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
mheinzl
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diff changeset
262 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
parents: 5
diff changeset
263 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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diff changeset
264
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
265 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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diff changeset
266 if fs == 21:
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
267 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
268 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
269 fs = "={}".format(fs)
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
270 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
mheinzl
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diff changeset
271 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
272
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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diff changeset
273 else:
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
274 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
275 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
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
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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
mheinzl
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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(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
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])), 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
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 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
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diff changeset
284 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
mheinzl
parents: 3
diff changeset
285 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
mheinzl
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diff changeset
286 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
mheinzl
parents: 3
diff changeset
287 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
mheinzl
parents: 3
diff changeset
288 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
parents:
diff changeset
289 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
290 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
291 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
292 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
mheinzl
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diff changeset
293
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
294 print("Files successfully created!")
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff changeset
295
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
296
0
6716b1cddf3e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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diff changeset
297 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
298 sys.exit(compare_read_families_read_loss(sys.argv))