Mercurial > repos > cstrittmatter > test_eurl_vtec_wgs_pt

comparison scripts/fastq_positional_quality_trimming.py @ 3:0cbed1c0a762 draft default tip

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planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
author cstrittmatter
date Tue, 28 Jan 2020 10:42:31 -0500
parents 965517909457
children
comparison
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2:6837f733b4aa 3:0cbed1c0a762
88 passing_reads = 0 88 passing_reads = 0
89 trimmed_forward = open(options.trimmed1, 'w') 89 trimmed_forward = open(options.trimmed1, 'w')
90 log = open(options.logfile, 'w') 90 log = open(options.logfile, 'w')
91 try: 91 try:
92 while True: 92 while True:
93 headL = forward.next().rstrip() 93 headL = next(forward).rstrip()
94 sequL = forward.next().rstrip() 94 sequL = next(forward).rstrip()
95 commL = forward.next().rstrip() 95 commL = next(forward).rstrip()
96 sangL = forward.next().rstrip() 96 sangL = next(forward).rstrip()
97 qualL = sanger2phred(sangL) 97 qualL = sanger2phred(sangL)
98 trimmed_sequL, trimmed_qualL = trimming(sequL, qualL, maxlengthtrim, lefttrim, righttrim, minqualtrim, avgqualtrim) 98 trimmed_sequL, trimmed_qualL = trimming(sequL, qualL, maxlengthtrim, lefttrim, righttrim, minqualtrim, avgqualtrim)
99 if paired: 99 if paired:
100 try: 100 try:
101 headR = reverse.next().rstrip() 101 headR = next(reverse).rstrip()
102 sequR = reverse.next().rstrip() 102 sequR = next(reverse).rstrip()
103 commR = reverse.next().rstrip() 103 commR = next(reverse).rstrip()
104 sangR = reverse.next().rstrip() 104 sangR = next(reverse).rstrip()
105 except StopIteration: 105 except StopIteration:
106 sys.exit('Reverse FASTQ file contain less reads than forward FASTQ file.') 106 sys.exit('Reverse FASTQ file contain less reads than forward FASTQ file.')
107 qualR = sanger2phred(sangR) 107 qualR = sanger2phred(sangR)
108 trimmed_sequR, trimmed_qualR = trimming(sequR, qualR, maxlengthtrim, lefttrim, righttrim, minqualtrim, avgqualtrim) 108 trimmed_sequR, trimmed_qualR = trimming(sequR, qualR, maxlengthtrim, lefttrim, righttrim, minqualtrim, avgqualtrim)
109 # Filter by residual length 109 # Filter by residual length
128 discarded_reads += 1 128 discarded_reads += 1
129 total_reads += 1 129 total_reads += 1
130 except StopIteration: 130 except StopIteration:
131 if paired: 131 if paired:
132 try: 132 try:
133 reverse.next() 133 next(reverse)
134 except StopIteration: 134 except StopIteration:
135 log.write("Total paired reads : %d\n" % total_reads) 135 log.write("Total paired reads : %d\n" % total_reads)
136 log.write("Passing paired reads : %d\n" % passing_paired_reads) 136 log.write("Passing paired reads : %d\n" % passing_paired_reads)
137 log.write("Passing unpaired reads : %d\n" % passing_unpaired_reads) 137 log.write("Passing unpaired reads : %d\n" % passing_unpaired_reads)
138 log.write("Discarded paired reads : %d\n" % discarded_reads) 138 log.write("Discarded paired reads : %d\n" % discarded_reads)