Mercurial > repos > cstrittmatter > test_eurl_vtec_wgs_pt
diff scripts/fastq_positional_quality_trimming.py @ 3:0cbed1c0a762 draft default tip
planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
author | cstrittmatter |
---|---|
date | Tue, 28 Jan 2020 10:42:31 -0500 |
parents | 965517909457 |
children |
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--- a/scripts/fastq_positional_quality_trimming.py Wed Jan 22 09:10:12 2020 -0500 +++ b/scripts/fastq_positional_quality_trimming.py Tue Jan 28 10:42:31 2020 -0500 @@ -90,18 +90,18 @@ log = open(options.logfile, 'w') try: while True: - headL = forward.next().rstrip() - sequL = forward.next().rstrip() - commL = forward.next().rstrip() - sangL = forward.next().rstrip() + headL = next(forward).rstrip() + sequL = next(forward).rstrip() + commL = next(forward).rstrip() + sangL = next(forward).rstrip() qualL = sanger2phred(sangL) trimmed_sequL, trimmed_qualL = trimming(sequL, qualL, maxlengthtrim, lefttrim, righttrim, minqualtrim, avgqualtrim) if paired: try: - headR = reverse.next().rstrip() - sequR = reverse.next().rstrip() - commR = reverse.next().rstrip() - sangR = reverse.next().rstrip() + headR = next(reverse).rstrip() + sequR = next(reverse).rstrip() + commR = next(reverse).rstrip() + sangR = next(reverse).rstrip() except StopIteration: sys.exit('Reverse FASTQ file contain less reads than forward FASTQ file.') qualR = sanger2phred(sangR) @@ -130,7 +130,7 @@ except StopIteration: if paired: try: - reverse.next() + next(reverse) except StopIteration: log.write("Total paired reads : %d\n" % total_reads) log.write("Passing paired reads : %d\n" % passing_paired_reads)