"""MultiQC module to parse output from Slamdunk"""

import logging
import re

from multiqc import config
from multiqc.base_module import BaseMultiqcModule, ModuleNoSamplesFound
from multiqc.plots import bargraph, linegraph, scatter, table

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

VERSION_REGEX = r"# slamdunk summary v([\d\.]+)"


class MultiqcModule(BaseMultiqcModule):
    """
    Slamdunk module class, parses slamdunk logs.
    """

    def __init__(self):
        # Initialise the parent object
        super(MultiqcModule, self).__init__(
            name="Slamdunk",
            anchor="slamdunk",
            href="http://t-neumann.github.io/slamdunk/",
            info="is a tool to analyze SLAMSeq data.",
            doi="10.1186/s12859-019-2849-7",
        )

        num_reports = 0

        self.plot_cols = [
            "#fdbf6f",
            "#2171B5",
            "#6BAED6",
            "#C6DBEF",
            "#74C476",
            "#C7E9C0",
            "#D9D9D9",
            "#969696",
            "#525252",
            "#DADAEB",
            "#9E9AC8",
            "#6A51A3",
        ]

        # Summary Reports
        self.slamdunk_data = dict()
        for f in self.find_log_files("slamdunk/summary", filehandles=True):
            self.parseSummary(f)
        self.slamdunk_data = self.ignore_samples(self.slamdunk_data)
        if len(self.slamdunk_data) > 0:
            self.slamdunkGeneralStatsTable()
            self.slamdunkFilterStatsTable()
            log.debug(f"Found {len(self.slamdunk_data)} summary reports")
            num_reports = max(num_reports, len(self.slamdunk_data))

        # PCA Plots
        self.PCA_data = dict()
        for f in self.find_log_files("slamdunk/PCA", filehandles=True):
            self.parsePCA(f)
        self.PCA_data = self.ignore_samples(self.PCA_data)
        if len(self.PCA_data) > 0:
            self.slamdunkPCAPlot()
            log.debug(f"Found {len(self.PCA_data)} PCA plots")
            num_reports = max(num_reports, len(self.PCA_data))

        # UTR Rate reports
        self.utrates_data = dict()
        for f in self.find_log_files("slamdunk/utrrates", filehandles=True):
            self.parseUtrRates(f)
        self.utrates_data = self.ignore_samples(self.utrates_data)
        if len(self.utrates_data) > 0:
            self.write_data_file(self.utrates_data, "multiqc_slamdunk_utrrates")
            self.slamdunkUtrRatesPlot()
            log.debug(f"Found {len(self.utrates_data)} UTR rate reports")
            num_reports = max(num_reports, len(self.utrates_data))

        # Read rate reports
        self.rates_data_plus = dict()
        self.rates_data_minus = dict()
        for f in self.find_log_files("slamdunk/rates", filehandles=True):
            self.parseSlamdunkRates(f)
        self.rates_data_plus = self.ignore_samples(self.rates_data_plus)
        self.rates_data_minus = self.ignore_samples(self.rates_data_minus)
        if len(self.rates_data_plus) > 0:
            self.write_data_file(self.rates_data_plus, "multiqc_slamdunk_readrates_plus")
            self.write_data_file(self.rates_data_minus, "multiqc_slamdunk_readrates_minus")
            self.slamdunkOverallRatesPlot()
            log.debug(f"Found {len(self.rates_data_plus)} read rate reports")
            num_reports = max(num_reports, len(self.rates_data_plus))

        # TCP error read rate
        self.nontc_per_readpos_plus = dict()
        self.nontc_per_readpos_minus = dict()
        self.tc_per_readpos_plus = dict()
        self.tc_per_readpos_minus = dict()
        for f in self.find_log_files("slamdunk/tcperreadpos", filehandles=True):
            self.parseSlamdunkTCPerReadpos(f)
        self.nontc_per_readpos_plus = self.ignore_samples(self.nontc_per_readpos_plus)
        self.nontc_per_readpos_minus = self.ignore_samples(self.nontc_per_readpos_minus)
        self.tc_per_readpos_plus = self.ignore_samples(self.tc_per_readpos_plus)
        self.tc_per_readpos_minus = self.ignore_samples(self.tc_per_readpos_minus)
        if len(self.tc_per_readpos_plus) > 0:
            self.write_data_file(self.tc_per_readpos_plus, "multiqc_slamdunk_tcperreadpos_plus")
            self.write_data_file(self.nontc_per_readpos_plus, "multiqc_slamdunk_nontcperreadpos_plus")
            self.write_data_file(self.tc_per_readpos_minus, "multiqc_slamdunk_tcperreadpos_minus")
            self.write_data_file(self.nontc_per_readpos_minus, "multiqc_slamdunk_nontcperreadpos_minus")
            self.slamdunkTcPerReadPosPlot()
            log.debug(f"Found {len(self.tc_per_readpos_plus)} TCP error read rate reports")
            num_reports = max(num_reports, len(self.tc_per_readpos_plus))

        # Non-TCP error read rate
        self.nontc_per_utrpos_plus = dict()
        self.nontc_per_utrpos_minus = dict()
        self.tc_per_utrpos_plus = dict()
        self.tc_per_utrpos_minus = dict()
        for f in self.find_log_files("slamdunk/tcperutrpos", filehandles=True):
            self.parseSlamdunkTCPerUtrpos(f)
        self.nontc_per_utrpos_plus = self.ignore_samples(self.nontc_per_utrpos_plus)
        self.nontc_per_utrpos_minus = self.ignore_samples(self.nontc_per_utrpos_minus)
        self.tc_per_utrpos_plus = self.ignore_samples(self.tc_per_utrpos_plus)
        self.tc_per_utrpos_minus = self.ignore_samples(self.tc_per_utrpos_minus)
        if len(self.nontc_per_utrpos_plus) > 0:
            self.write_data_file(self.tc_per_utrpos_plus, "multiqc_slamdunk_tcperutrpos_plus")
            self.write_data_file(self.nontc_per_utrpos_plus, "multiqc_slamdunk_nontcperutrpos_plus")
            self.write_data_file(self.tc_per_utrpos_minus, "multiqc_slamdunk_tcperutrpos_minus")
            self.write_data_file(self.nontc_per_utrpos_minus, "multiqc_slamdunk_nontcperutrpos_minus")
            self.slamdunkTcPerUTRPosPlot()
            log.debug(f"Found {len(self.nontc_per_utrpos_plus)} non TCP error read rate reports")
            num_reports = max(num_reports, len(self.nontc_per_utrpos_plus))

        if num_reports == 0:
            raise ModuleNoSamplesFound
        else:
            log.info(f"Found {num_reports} reports")

    def parsePCA(self, f):
        # Skip header
        next(f["f"])

        for line in f["f"]:
            fields = line.rstrip().split("\t")

            sample = self.clean_s_name(fields[0], f)
            PC1 = fields[1]
            PC2 = fields[2]

            self.PCA_data[sample] = [{"x": float(PC1), "y": float(PC2)}]

    def parseUtrRates(self, f):
        # Skip comment line #
        next(f["f"])

        # Read median header
        line = next(f["f"])

        if "Conversions=" in line:
            sample = f["s_name"]
            self.utrates_data[sample] = dict()

            conversions = re.sub(".*Conversions=", "", line.rstrip()).split(",")

            for conversion in conversions:
                type, value = conversion.split(":")
                self.utrates_data[sample][type] = float(value)

        else:
            log.warning("Malformed UTR rates header. Conversion rates per UTR plot will be affected.")

    def parseSlamdunkRates(self, f):
        sample = f["s_name"]

        # Skip comment line #
        next(f["f"])

        bases = next(f["f"]).rstrip().split("\t")

        baseDict = {}
        order = {}

        for i in range(1, len(bases)):
            order[i] = bases[i]

        for line in f["f"]:
            values = line.rstrip().split("\t")
            base = values[0]
            baseDict[base] = {}

            for i in range(1, len(values)):
                baseDict[base][order[i]] = int(values[i])

        divisor = {}

        for fromBase in baseDict:
            for toBase in baseDict[fromBase]:
                if toBase.islower():
                    if fromBase.lower() not in divisor:
                        divisor[fromBase.lower()] = 0
                    divisor[fromBase.lower()] += baseDict[fromBase][toBase]
                else:
                    if fromBase not in divisor:
                        divisor[fromBase] = 0
                    divisor[fromBase] += baseDict[fromBase][toBase]

        for fromBase in baseDict:
            for toBase in baseDict[fromBase]:
                if toBase.islower():
                    if divisor[fromBase.lower()] > 0:
                        baseDict[fromBase][toBase] = baseDict[fromBase][toBase] / float(divisor[fromBase.lower()]) * 100
                    else:
                        baseDict[fromBase][toBase] = 0.0
                else:
                    if divisor[fromBase] > 0:
                        baseDict[fromBase][toBase] = baseDict[fromBase][toBase] / float(divisor[fromBase]) * 100
                    else:
                        baseDict[fromBase][toBase] = 0.0

        self.rates_data_plus[sample] = {}
        self.rates_data_minus[sample] = {}

        for fromBase in baseDict:
            for toBase in baseDict[fromBase]:
                if fromBase != "N" and toBase.upper() != "N" and fromBase != toBase.upper():
                    if toBase.islower():
                        self.rates_data_minus[sample][fromBase + ">" + toBase.upper()] = baseDict[fromBase][toBase]
                    else:
                        self.rates_data_plus[sample][fromBase + ">" + toBase] = baseDict[fromBase][toBase]

    def parseSlamdunkTCPerReadpos(self, f):
        sample = f["s_name"]

        # Skip comment line #
        next(f["f"])

        self.nontc_per_readpos_plus[sample] = {}
        self.nontc_per_readpos_minus[sample] = {}

        self.tc_per_readpos_plus[sample] = {}
        self.tc_per_readpos_minus[sample] = {}

        pos = 1

        for line in f["f"]:
            values = line.rstrip().split("\t")
            if int(values[4]) > 0:
                self.nontc_per_readpos_plus[sample][pos] = float(int(values[0])) / int(values[4]) * 100
                self.tc_per_readpos_plus[sample][pos] = float(int(values[2])) / int(values[4]) * 100
            else:
                self.nontc_per_readpos_plus[sample][pos] = 0
                self.tc_per_readpos_plus[sample][pos] = 0

            if int(values[5]) > 0:
                self.nontc_per_readpos_minus[sample][pos] = float(int(values[1])) / int(values[5]) * 100
                self.tc_per_readpos_minus[sample][pos] = float(int(values[3])) / int(values[5]) * 100
            else:
                self.nontc_per_readpos_minus[sample][pos] = 0
                self.tc_per_readpos_minus[sample][pos] = 0

            pos += 1

    def parseSlamdunkTCPerUtrpos(self, f):
        sample = f["s_name"]

        # Skip comment line #
        next(f["f"])

        self.nontc_per_utrpos_plus[sample] = {}
        self.nontc_per_utrpos_minus[sample] = {}

        self.tc_per_utrpos_plus[sample] = {}
        self.tc_per_utrpos_minus[sample] = {}

        pos = 1

        for line in f["f"]:
            values = line.rstrip().split("\t")
            if int(values[4]) > 0:
                self.nontc_per_utrpos_plus[sample][pos] = float(int(values[0])) / int(values[4]) * 100
                self.tc_per_utrpos_plus[sample][pos] = float(int(values[2])) / int(values[4]) * 100
            else:
                self.nontc_per_utrpos_plus[sample][pos] = 0
                self.tc_per_utrpos_plus[sample][pos] = 0

            if int(values[5]) > 0:
                self.nontc_per_utrpos_minus[sample][pos] = float(int(values[1])) / int(values[5]) * 100
                self.tc_per_utrpos_minus[sample][pos] = float(int(values[3])) / int(values[5]) * 100
            else:
                self.nontc_per_utrpos_minus[sample][pos] = 0
                self.tc_per_utrpos_minus[sample][pos] = 0

            pos += 1

    def parseSummary(self, f):
        # Parse version form first line
        first = next(f["f"])
        version = None
        match = re.search(VERSION_REGEX, first)
        if match:
            version = match.group(1)

        # Skip header line "FileName..."
        columnCount = next(f["f"]).count("\t") + 1

        for line in f["f"]:
            fields = line.rstrip().split("\t")
            s_name = self.clean_s_name(fields[0], f)
            self.slamdunk_data[s_name] = dict()
            self.slamdunk_data[s_name]["sequenced"] = int(fields[4])
            self.slamdunk_data[s_name]["mapped"] = int(fields[5])
            # self.slamdunk_data[s_name]['deduplicated'] = int(fields[6])
            self.slamdunk_data[s_name]["mqfiltered"] = int(fields[7])
            self.slamdunk_data[s_name]["idfiltered"] = int(fields[8])
            self.slamdunk_data[s_name]["nmfiltered"] = int(fields[9])
            self.slamdunk_data[s_name]["multimapper"] = int(fields[10])
            self.slamdunk_data[s_name]["retained"] = int(fields[11])

            # Additional Count Column found in Table
            if columnCount == 14:
                self.slamdunk_data[s_name]["counted"] = int(fields[12])

        for s_name in self.slamdunk_data.keys():
            self.add_software_version(version, s_name)
            self.add_data_source(f, s_name=s_name)

    def slamdunkGeneralStatsTable(self):
        """Take the parsed summary stats from Slamdunk and add it to the
        basic stats table at the top of the report"""

        headers = {
            "counted": {
                "title": f"{config.read_count_prefix} Counted",
                "description": f"# reads counted within 3'UTRs ({config.read_count_desc})",
                "shared_key": "read_count",
                "min": 0,
                "format": "{:,.2f}",
                "scale": "YlGn",
                "modify": lambda x: float(x) * config.read_count_multiplier,
            },
            "retained": {
                "title": f"{config.read_count_prefix} Retained",
                "description": f"# retained reads after filtering ({config.read_count_desc})",
                "shared_key": "read_count",
                "min": 0,
                "format": "{:,.2f}",
                "scale": "YlGn",
                "modify": lambda x: float(x) * config.read_count_multiplier,
            },
            "mapped": {
                "title": f"{config.read_count_prefix} Mapped",
                "description": f"# mapped reads ({config.read_count_desc})",
                "shared_key": "read_count",
                "min": 0,
                "format": "{:,.2f}",
                "scale": "YlGn",
                "modify": lambda x: float(x) * config.read_count_multiplier,
            },
            "sequenced": {
                "title": f"{config.read_count_prefix} Sequenced",
                "description": f"# sequenced reads ({config.read_count_desc})",
                "shared_key": "read_count",
                "min": 0,
                "format": "{:,.2f}",
                "scale": "YlGn",
                "modify": lambda x: float(x) * config.read_count_multiplier,
            },
        }

        self.general_stats_addcols(self.slamdunk_data, headers)

    def slamdunkFilterStatsTable(self):
        """Take the parsed filter stats from Slamdunk and add it to a separate table"""

        headers = {
            "mapped": {
                "namespace": "Slamdunk",
                "title": f"{config.read_count_prefix} Mapped",
                "description": f"# mapped reads ({config.read_count_desc})",
                "shared_key": "read_count",
                "min": 0,
                "format": "{:,.2f}",
                "suffix": config.read_count_prefix,
                "scale": "YlGn",
                "modify": lambda x: float(x) * config.read_count_multiplier,
            },
            "multimapper": {
                "namespace": "Slamdunk",
                "title": f"{config.read_count_prefix} Multimap-Filtered",
                "description": f"# multimap-filtered reads ({config.read_count_desc})",
                "shared_key": "read_count",
                "min": 0,
                "format": "{:,.2f}",
                "suffix": config.read_count_prefix,
                "scale": "OrRd",
                "modify": lambda x: float(x) * config.read_count_multiplier,
            },
            "nmfiltered": {
                "namespace": "Slamdunk",
                "title": f"{config.read_count_prefix} NM-Filtered",
                "description": f"# NM-filtered reads ({config.read_count_desc})",
                "shared_key": "read_count",
                "min": 0,
                "format": "{:,.2f}",
                "suffix": config.read_count_prefix,
                "scale": "OrRd",
                "modify": lambda x: float(x) * config.read_count_multiplier,
            },
            "idfiltered": {
                "namespace": "Slamdunk",
                "title": f"{config.read_count_prefix} Identity-Filtered",
                "description": f"# identity-filtered reads ({config.read_count_desc})",
                "shared_key": "read_count",
                "min": 0,
                "format": "{:,.2f}",
                "suffix": config.read_count_prefix,
                "scale": "OrRd",
                "modify": lambda x: float(x) * config.read_count_multiplier,
            },
            "mqfiltered": {
                "namespace": "Slamdunk",
                "title": f"{config.read_count_prefix} MQ-Filtered",
                "description": f"# MQ-filtered reads ({config.read_count_desc})",
                "shared_key": "read_count",
                "min": 0,
                "format": "{:,.2f}",
                "suffix": config.read_count_prefix,
                "scale": "OrRd",
                "modify": lambda x: float(x) * config.read_count_multiplier,
            },
        }
        pconfig = {
            "id": "slamdunk_filtering_table",
            "min": 0,
            "title": "Slamdunk: Filtering statistics",
        }

        self.add_section(
            name="Filter statistics",
            anchor="slamdunk_filtering",
            description="This table shows the number of reads filtered with each filter criterion during filtering phase of slamdunk.",
            plot=table.plot(self.slamdunk_data, headers, pconfig),
        )

    def slamdunkOverallRatesPlot(self):
        """Generate the overall rates plot"""

        pconfig = {
            "id": "overallratesplot",
            "title": "Slamdunk: Overall conversion rates in reads",
            "cpswitch": False,
            "cpswitch_c_active": False,
            "ylab": "Number of reads",
            "stacking": "normal",
            "tt_decimals": 2,
            "tt_suffix": "%",
            "hide_zero_cats": False,
            "data_labels": [
                "Plus Strand +",
                "Minus Strand -",
            ],
        }

        cats = [dict(), dict()]
        keys = [
            ["T>C", "A>T", "A>G", "A>C", "T>A", "T>G", "G>A", "G>T", "G>C", "C>A", "C>T", "C>G"],
            ["A>G", "A>T", "A>C", "T>A", "T>G", "T>C", "G>A", "G>T", "G>C", "C>A", "C>T", "C>G"],
        ]
        for i, k in enumerate(keys):
            for j, v in enumerate(k):
                cats[i][v] = {"color": self.plot_cols[j]}

        self.add_section(
            name="Conversion rates per read",
            anchor="slamdunk_overall_rates",
            description="""This plot shows the individual conversion rates over all reads.
                        It shows these conversion rates strand-specific: This means for a properly labeled
                        sample you would see a T&gt;C excess on the plus-strand and an A&gt;G excess on the minus strand
                        (see the <a href="http://t-neumann.github.io/slamdunk/docs.html#rates" target="_blank">slamdunk docs</a>).""",
            plot=bargraph.plot([self.rates_data_plus, self.rates_data_minus], cats, pconfig),
        )

    def slamdunkUtrRatesPlot(self):
        """Generate the UTR rates plot"""

        cats = dict()
        keys = ["T>C", "A>T", "A>G", "A>C", "T>A", "T>G", "G>A", "G>T", "G>C", "C>A", "C>T", "C>G"]
        for i, v in enumerate(keys):
            cats[v] = {"color": self.plot_cols[i]}

        pconfig = {
            "id": "slamdunk_utrratesplot",
            "title": "Slamdunk: Overall conversion rates per UTR",
            "cpswitch": False,
            "cpswitch_c_active": False,
            "ylab": "Number of conversions",
            "stacking": "normal",
            "tt_decimals": 2,
            "tt_suffix": "%",
            "hide_zero_cats": False,
        }

        self.add_section(
            name="Conversion rates per UTR",
            anchor="slamdunk_utr_rates",
            description="""This plot shows the individual conversion rates for all UTRs
                        (see the <a href="http://t-neumann.github.io/slamdunk/docs.html#utrrates" target="_blank">slamdunk docs</a>).""",
            plot=bargraph.plot(self.utrates_data, cats, pconfig),
        )

    def slamdunkPCAPlot(self):
        """Generate the PCA plots"""

        pconfig = {
            "id": "slamdunk_pca",
            "title": "Slamdunk: PCA",
            "xlab": "PC1",
            "ylab": "PC2",
            "tt_label": "PC1 {point.x:.2f}: PC2 {point.y:.2f}",
        }

        self.add_section(
            name="PCA (T&gt;C based)",
            anchor="slamdunk_PCA",
            description="""This plot shows the principal components of samples based
                        on the distribution of reads with T&gt;C conversions within UTRs
                        (see the <a href="http://t-neumann.github.io/slamdunk/docs.html#summary" target="_blank">slamdunk docs</a>).""",
            plot=scatter.plot(self.PCA_data, pconfig),
        )

    def slamdunkTcPerReadPosPlot(self):
        """Generate the tc per read pos plots"""

        pconfig_nontc = {
            "id": "slamdunk_nontcperreadpos_plot",
            "title": "Slamdunk: Non-T>C mismatches over reads",
            "ylab": "Percent mismatches %",
            "xlab": "Position in read",
            "xDecimals": False,
            "ymin": 0,
            "tt_label": "<b>Pos {point.x}</b>: {point.y:.2f} %",
            "data_labels": [
                {"name": "Forward reads +", "ylab": "Percent mismatches %"},
                {"name": "Reverse reads -", "ylab": "Percent mismatches %"},
            ],
        }

        pconfig_tc = {
            "id": "slamdunk_tcperreadpos_plot",
            "title": "Slamdunk: T>C conversions over reads",
            "ylab": "Percent converted %",
            "xlab": "Position in read",
            "xDecimals": False,
            "ymin": 0,
            "tt_label": "<b>Pos {point.x}</b>: {point.y:.2f} %",
            "data_labels": [
                {"name": "Forward reads +", "ylab": "Percent converted %"},
                {"name": "Reverse reads -", "ylab": "Percent converted %"},
            ],
        }

        self.add_section(
            name="Non T&gt;C mismatches over read positions",
            anchor="slamdunk_nontcperreadpos",
            description="""This plot shows the distribution of non T&gt;C mismatches across read positions
                        (see the <a href="http://t-neumann.github.io/slamdunk/docs.html#tcperreadpos" target="_blank">slamdunk docs</a>).""",
            plot=linegraph.plot([self.nontc_per_readpos_plus, self.nontc_per_readpos_minus], pconfig_nontc),
        )

        self.add_section(
            name="T&gt;C conversions over read positions",
            anchor="slamdunk_tcperreadpos",
            description="""This plot shows the distribution of T&gt;C conversions across read positions
                        (see the <a href="http://t-neumann.github.io/slamdunk/docs.html#tcperreadpos" target="_blank">slamdunk docs</a>).""",
            plot=linegraph.plot([self.tc_per_readpos_plus, self.tc_per_readpos_minus], pconfig_tc),
        )

    def slamdunkTcPerUTRPosPlot(self):
        """Generate the tc per UTR pos plots"""

        pconfig_nontc = {
            "id": "slamdunk_slamdunk_nontcperutrpos_plot",
            "title": "Slamdunk: Non-T>C mutations over 3' UTR ends",
            "ylab": "Percent mismatches %",
            "xlab": "Position in the static last 250bp window of 3' UTR",
            "xDecimals": False,
            "ymin": 0,
            "tt_label": "<b>Pos {point.x}</b>: {point.y:.2f} %",
            "data_labels": [
                {"name": "UTRs on plus strand", "ylab": "Percent mismatches %"},
                {"name": "UTRs on minus strand", "ylab": "Percent mismatches %"},
            ],
        }

        pconfig_tc = {
            "id": "slamdunk_slamdunk_tcperutrpos_plot",
            "title": "Slamdunk: T>C conversions over 3' UTR ends",
            "ylab": "Percent converted %",
            "xlab": "Position in the static last 250bp window of 3' UTR",
            "xDecimals": False,
            "ymin": 0,
            "tt_label": "<b>Pos {point.x}</b>: {point.y:.2f} %",
            "data_labels": [
                {"name": "UTRs on plus strand", "ylab": "Percent converted %"},
                {"name": "UTRs on minus strand", "ylab": "Percent converted %"},
            ],
        }

        self.add_section(
            name="Non T&gt;C mismatches over UTR positions",
            anchor="slamdunk_nontcperutrpos",
            description="""This plot shows the distribution of non T&gt;C mismatches across UTR positions for the last 250 bp from the 3\' UTR end
                        (see the <a href="http://t-neumann.github.io/slamdunk/docs.html#tcperutrpos" target="_blank">slamdunk docs</a>).""",
            plot=linegraph.plot([self.nontc_per_utrpos_plus, self.nontc_per_utrpos_minus], pconfig_nontc),
        )

        self.add_section(
            name="T&gt;C conversions over UTR positions",
            anchor="tcperutrpos",
            description="""This plot shows the distribution of T&gt;C conversions across UTR positions for the last 250 bp from the 3\' UTR end
                        (see the <a href="http://t-neumann.github.io/slamdunk/docs.html#tcperutrpos" target="_blank">slamdunk docs</a>).""",
            plot=linegraph.plot([self.tc_per_utrpos_plus, self.tc_per_utrpos_minus], pconfig_tc),
        )
