comparison vsnp_statistics.py @ 21:377c1a96aae9 draft

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20:d4ef7003c539

    else:
        columns = ['Reference', 'FASTQ', 'File Size', 'Mean Read Length', 'Mean Read Quality', 'Reads Passing Q30',
                   'Total Reads', 'All Mapped Reads', 'Unmapped Reads', 'Unmapped Reads Percentage of Total',
                   'Reference with Coverage', 'Average Depth of Coverage', 'Good SNP Count']
    with open(output_file, "w") as outfh:
        outfh.write("%s\n" % "\t".join(columns))
        line_items = []
        # Get the current stats and associated files.
        # Get and output the statistics.
        line_items.append(read1_stats.reference)
        line_items.append(read1_stats.fastq_file)

21:377c1a96aae9

    else:
        columns = ['Reference', 'FASTQ', 'File Size', 'Mean Read Length', 'Mean Read Quality', 'Reads Passing Q30',
                   'Total Reads', 'All Mapped Reads', 'Unmapped Reads', 'Unmapped Reads Percentage of Total',
                   'Reference with Coverage', 'Average Depth of Coverage', 'Good SNP Count']
    with open(output_file, "w") as outfh:
        # Make sure the header starts with a # so
        # MultiQC can properly handle the output.
        outfh.write("# %s\n" % "\t".join(columns))
        line_items = []
        # Get the current stats and associated files.
        # Get and output the statistics.
        line_items.append(read1_stats.reference)
        line_items.append(read1_stats.fastq_file)