Mercurial > repos > cstrittmatter > test_eurl_vtec_wgs_pt

annotate scripts/fastq_positional_quality_trimming.py @ 2:6837f733b4aa draft

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planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
author cstrittmatter
date Wed, 22 Jan 2020 09:10:12 -0500
parents 965517909457
children 0cbed1c0a762
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1 # -*- coding: utf-8 -*-
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2 """
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3 This tool trims paired-end FASTQ files on the basis of quality score or left/right position, retaining mate integrity.
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4 Reads without mate after filtering are saved in a separate output file.
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5 """
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6
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7 import math
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8 import optparse
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9 import sys
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10
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11 def average(values):
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12 """ Arithmetic mean of a list of values """
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13 return math.fsum(values) / len(values) if len(values) else float('nan')
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14
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15
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16 def phred2sanger(phred_scores):
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17 """ Convert an array of Phred quality scores (integers in [0, 93]) to a Sanger-encoded quality string"""
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18 return ''.join([chr(score + 33) for score in phred_scores])
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19
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20
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21 def sanger2phred(sanger_string):
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22 """ Convert a Sanger-encoded quality string to an array of Phred quality scores"""
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23 return [ord(ch) - 33 for ch in sanger_string]
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24
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25
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26 def trimming(sequ, qual, maxlengthtrim, lefttrim, righttrim, minqualtrim, avgqualtrim):
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27 """ Trimming of sequence and quality of a read"""
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28 # Maximum length trimming
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29 if maxlengthtrim != -1:
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30 if len(sequ) > maxlengthtrim:
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31 sequ = sequ[: maxlengthtrim]
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32 qual = qual[: maxlengthtrim]
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33 # Left- and right-side trimming
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34 if righttrim == 0:
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35 sequ = sequ[lefttrim :]
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36 qual = qual[lefttrim :]
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37 else:
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38 sequ = sequ[lefttrim : -righttrim]
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39 qual = qual[lefttrim : -righttrim]
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40 # Minimum quality right-side trimming
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41 while len(sequ) and qual[-1] < minqualtrim:
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42 qual = qual[:-1]
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43 sequ = sequ[:-1]
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44 # Average quality right-side trimming
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45 while len(sequ) and average(qual) < avgqualtrim:
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46 qual = qual[:-1]
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47 sequ = sequ[:-1]
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48 return sequ, qual
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49
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50
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51 def __main__():
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52 parser = optparse.OptionParser()
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53 parser.add_option('-1', '--input1', dest='input1', help='forward or single-end reads file in Sanger FASTQ format')
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54 parser.add_option('-2', '--input2', dest='input2', help='reverse reads file in Sanger FASTQ format')
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55 parser.add_option('--maxlt', dest='maxlengthtrim', type='int', default=400, help='maximum length trimming')
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56 parser.add_option('--lt', dest='lefttrim', type='int', default=0, help='left-side trimming')
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57 parser.add_option('--rt', dest='righttrim', type='int', default=0, help='right-side trimming')
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58 parser.add_option('--minqt', dest='minqualtrim', type='int', default=15, help='minimum quality right-side trimming')
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59 parser.add_option('--avgqt', dest='avgqualtrim', type='float', default=20, help='average quality right-side trimming')
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60 parser.add_option('--minlf', dest='minlen', type='int', default=25, help='minimum length filtering')
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61 parser.add_option('--trimmed1', dest='trimmed1', help='trimmed forward FASTQ file')
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62 parser.add_option('--trimmed2', dest='trimmed2', help='trimmed reverse FASTQ file')
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63 parser.add_option('--trimmedunpaired', dest='trimmedunpaired', help='trimmed unpaired FASTQ file')
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64 parser.add_option('--log', dest='logfile', help='log file')
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65 (options, args) = parser.parse_args()
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66 if len(args) > 0:
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67 parser.error('Wrong number of arguments')
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68
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69 maxlengthtrim = options.maxlengthtrim
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70 lefttrim = options.lefttrim
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71 righttrim = options.righttrim
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72 minqualtrim = options.minqualtrim
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73 avgqualtrim = options.avgqualtrim
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74 minlen = options.minlen
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75
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76 total_reads = 0
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77 discarded_reads = 0
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78 forward = open(options.input1)
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79 if options.input2:
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80 paired = True
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81 passing_paired_reads = 0
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82 passing_unpaired_reads = 0
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83 reverse = open(options.input2)
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84 trimmed_reverse = open(options.trimmed2, 'w')
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85 trimmed_unpaired = open(options.trimmedunpaired, 'w')
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86 else:
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87 paired = False
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88 passing_reads = 0
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89 trimmed_forward = open(options.trimmed1, 'w')
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90 log = open(options.logfile, 'w')
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91 try:
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92 while True:
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93 headL = forward.next().rstrip()
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94 sequL = forward.next().rstrip()
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95 commL = forward.next().rstrip()
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96 sangL = forward.next().rstrip()
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97 qualL = sanger2phred(sangL)
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98 trimmed_sequL, trimmed_qualL = trimming(sequL, qualL, maxlengthtrim, lefttrim, righttrim, minqualtrim, avgqualtrim)
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99 if paired:
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100 try:
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101 headR = reverse.next().rstrip()
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102 sequR = reverse.next().rstrip()
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103 commR = reverse.next().rstrip()
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104 sangR = reverse.next().rstrip()
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105 except StopIteration:
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106 sys.exit('Reverse FASTQ file contain less reads than forward FASTQ file.')
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107 qualR = sanger2phred(sangR)
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108 trimmed_sequR, trimmed_qualR = trimming(sequR, qualR, maxlengthtrim, lefttrim, righttrim, minqualtrim, avgqualtrim)
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109 # Filter by residual length
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110 if paired:
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111 if len(trimmed_sequL) >= minlen and len(trimmed_sequR) >= minlen:
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112 trimmed_forward.write(headL + '\n' + trimmed_sequL + '\n' + commL + '\n' + phred2sanger(trimmed_qualL) + '\n')
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113 trimmed_reverse.write(headR + '\n' + trimmed_sequR + '\n' + commR + '\n' + phred2sanger(trimmed_qualR) + '\n')
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114 passing_paired_reads += 1
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115 elif len(trimmed_sequL) >= minlen and len(trimmed_sequR) < minlen:
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116 trimmed_unpaired.write(headL + '\n' + trimmed_sequL + '\n' + commL + '\n' + phred2sanger(trimmed_qualL) + '\n')
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117 passing_unpaired_reads += 1
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118 elif len(trimmed_sequL) < minlen and len(trimmed_sequR) >= minlen:
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119 trimmed_unpaired.write(headR + '\n' + trimmed_sequR + '\n' + commR + '\n' + phred2sanger(trimmed_qualR) + '\n')
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120 passing_unpaired_reads += 1
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121 else:
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122 discarded_reads += 1
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123 else:
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124 if len(trimmed_sequL) >= minlen:
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125 trimmed_forward.write(headL + '\n' + trimmed_sequL + '\n' + commL + '\n' + phred2sanger(trimmed_qualL) + '\n')
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126 passing_reads += 1
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127 else:
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128 discarded_reads += 1
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129 total_reads += 1
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130 except StopIteration:
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131 if paired:
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132 try:
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133 reverse.next()
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134 except StopIteration:
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135 log.write("Total paired reads : %d\n" % total_reads)
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136 log.write("Passing paired reads : %d\n" % passing_paired_reads)
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137 log.write("Passing unpaired reads : %d\n" % passing_unpaired_reads)
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138 log.write("Discarded paired reads : %d\n" % discarded_reads)
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139 else:
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140 sys.exit('Forward FASTQ file contain less reads than reverse FASTQ file.')
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141 else:
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142 log.write("Total reads : %d\n" % total_reads)
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143 log.write("Passing reads : %d\n" % passing_reads)
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144 log.write("Discarded reads : %d\n" % discarded_reads)
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145 finally:
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146 forward.close()
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147 trimmed_forward.close()
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148 log.close()
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149 if paired:
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150 reverse.close()
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151 trimmed_reverse.close()
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152 trimmed_unpaired.close()
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153
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154
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155 if __name__ == "__main__":
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156 __main__()