How to use the dnaio.UnknownFileFormat function in dnaio

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github marcelm / cutadapt / src / cutadapt / __main__.py View on Github external
except CommandLineError as e:
        parser.error(str(e))
        return  # avoid IDE warnings below

    logger.info("Processing reads on %d core%s in %s mode ...",
        cores, 's' if cores > 1 else '',
        {False: 'single-end', True: 'paired-end'}[pipeline.paired])
    try:
        with runner as r:
            stats = r.run()
    except KeyboardInterrupt:
        print("Interrupted", file=sys.stderr)
        sys.exit(130)
    except BrokenPipeError:
        sys.exit(1)
    except (dnaio.FileFormatError, dnaio.UnknownFileFormat, EOFError) as e:
        sys.exit("cutadapt: error: {}".format(e))

    elapsed = time.time() - start_time
    if args.report == 'minimal':
        report = minimal_report
    else:
        report = full_report
    logger.log(REPORT, '%s', report(stats, elapsed, args.gc_content / 100))
    if profiler is not None:
        import pstats
        profiler.disable()
        pstats.Stats(profiler).sort_stats('time').print_stats(20)

dnaio

Read and write FASTA and FASTQ files efficiently

MIT
Latest version published 10 days ago

Package Health Score

75 / 100
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