"""MultiQC module to parse TsTv by quality output from vcftools TsTv-by-qual"""

import logging

from multiqc.plots import linegraph

# Initialise the logger
log = logging.getLogger(__name__)


class TsTvByQualMixin:
    def parse_tstv_by_qual(self):
        """Create the HTML for the TsTv by quality linegraph plot."""

        self.vcftools_tstv_by_qual = dict()
        for f in self.find_log_files("vcftools/tstv_by_qual", filehandles=True):
            d = {}
            for line in f["f"].readlines()[1:]:  # don't add the header line (first row)
                key = float(line.split()[0])  # taking the first column (QUAL_THRESHOLD) as key
                val = float(line.split()[6])  # taking Ts/Tv_GT_QUAL_THRESHOLD as value
                if (val == float("inf")) or (val == float("-inf")):
                    val = float("nan")
                d[key] = val
            self.vcftools_tstv_by_qual[f["s_name"]] = d
            self.add_data_source(f, "TsTv by quality")

            # Superfluous function call to confirm that it is used in this module
            # Replace None with actual version if it is available
            self.add_software_version(None, f["s_name"])

        # Filter out ignored sample names
        self.vcftools_tstv_by_qual = self.ignore_samples(self.vcftools_tstv_by_qual)

        if len(self.vcftools_tstv_by_qual) == 0:
            return 0
        # Write data to file
        self.write_data_file(self.vcftools_tstv_by_qual, "vcftools_tstv_by_qual")

        pconfig = {
            "id": "vcftools_tstv_by_qual",
            "title": "VCFTools: TsTv by Qual",
            "ylab": "TsTv Ratio",
            "xlab": "SNP Quality Threshold",
            "xmin": 0,
            "ymin": 0,
            "smooth_points": 400,  # this limits huge filesizes and prevents browser crashing
            "smooth_points_sumcounts": False,
        }

        helptext = """
        `Transition` is a purine-to-purine or pyrimidine-to-pyrimidine point mutations.
        `Transversion` is a purine-to-pyrimidine or pyrimidine-to-purine point mutation.
        `Quality` here is the Phred-scaled quality score as given in the QUAL column of VCF.
        Note: only bi-allelic SNPs are used (multi-allelic sites and INDELs are skipped.)
        Refer to Vcftools's manual (https://vcftools.github.io/man_latest.html) on `--TsTv-by-qual`
        """

        self.add_section(
            name="TsTv by Qual",
            anchor="vcftools-tstv-by-qual",
            description="Plot of `TSTV-BY-QUAL` - the transition to transversion ratio as a function of SNP quality from the output of vcftools TsTv-by-qual.",
            helptext=helptext,
            plot=linegraph.plot(self.vcftools_tstv_by_qual, pconfig),
        )

        return len(self.vcftools_tstv_by_qual)
