comparison vsnp_statistics.py @ 23:b34843f09f9f draft

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22:61239720da38

def output_statistics(read1_stats, read2_stats, idxstats_file, metrics_file, output_file):
    paired_reads = read2_stats is not None
    if paired_reads:
        columns = ['Reference', 'Read1 FASTQ', 'File Size', 'Reads', 'Mean Read Length', 'Mean Read Quality',
                   'Reads Passing Q30', 'Read2 FASTQ', 'File Size', 'Reads', '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']
    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)
        line_items.append(read1_stats.file_size)
        if paired_reads:
            line_items.append(read1_stats.total_reads)
        line_items.append(read1_stats.mean_read_length)

        # Reference with Coverage
        ref_with_coverage, avg_depth_of_coverage, good_snp_count = process_metrics_file(metrics_file)
        line_items.append(ref_with_coverage)
        line_items.append(avg_depth_of_coverage)
        line_items.append(good_snp_count)
        outfh.write('%s\n' % '\t'.join(str(x) for x in line_items))


def process_idxstats_file(idxstats_file):
    all_mapped_reads = 0

23:b34843f09f9f

def output_statistics(read1_stats, read2_stats, idxstats_file, metrics_file, output_file):
    paired_reads = read2_stats is not None
    if paired_reads:
        columns = ['Read1 FASTQ', 'File Size', 'Reads', 'Mean Read Length', 'Mean Read Quality',
                   'Reads Passing Q30', 'Read2 FASTQ', 'File Size', 'Reads', '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', 'Reference']
    else:
        columns = ['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', 'Reference']
    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.fastq_file)
        line_items.append(read1_stats.file_size)
        if paired_reads:
            line_items.append(read1_stats.total_reads)
        line_items.append(read1_stats.mean_read_length)

        # Reference with Coverage
        ref_with_coverage, avg_depth_of_coverage, good_snp_count = process_metrics_file(metrics_file)
        line_items.append(ref_with_coverage)
        line_items.append(avg_depth_of_coverage)
        line_items.append(good_snp_count)
        line_items.append(read1_stats.reference)
        outfh.write('%s\n' % '\t'.join(str(x) for x in line_items))


def process_idxstats_file(idxstats_file):
    all_mapped_reads = 0