"""MultiQC module to parse output from HOMER tagdirectory"""

import logging
import math
import os
import re

from multiqc.plots import bargraph, linegraph

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


class TagDirReportMixin:
    def homer_tagdirectory(self):
        """Find HOMER tagdirectory logs and parse their data"""
        self.parse_gc_content()
        self.parse_re_dist()
        self.parse_tag_length_dist()
        self.parse_tagInfo_data()
        self.parse_freq_distribution_data()
        self.homer_stats_table_tagInfo()

        # 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)

        # Write data to file
        self.write_data_file(self.tagdir_data, "homer_tagdir")

        return sum([len(v) for k, v in self.tagdir_data.items() if k != "header"])

    def parse_gc_content(self):
        """parses and plots GC content and genome GC content files"""
        # Find and parse GC content:
        for f in self.find_log_files("homer/GCcontent", filehandles=True):
            # Get the s_name from the parent directory
            s_name = os.path.basename(f["root"])
            s_name = self.clean_s_name(s_name, f)
            parsed_data = self.parse_twoCol_file(f)
            if parsed_data is not None:
                if s_name in self.tagdir_data["GCcontent"]:
                    log.debug(f"Duplicate GCcontent sample log found! Overwriting: {s_name}")

                self.add_data_source(f, s_name, section="GCcontent")
                self.tagdir_data["GCcontent"][s_name] = parsed_data

        ## get esimated genome content distribution:
        for f in self.find_log_files("homer/genomeGCcontent", filehandles=True):
            parsed_data = self.parse_twoCol_file(f)
            if parsed_data is not None:
                if s_name + "_genome" in self.tagdir_data["GCcontent"]:
                    log.debug(f"Duplicate genome GCcontent sample log found! Overwriting: {s_name + '_genome'}")

                self.add_data_source(f, s_name + "_genome", section="GCcontent")
                self.tagdir_data["GCcontent"][s_name + "_genome"] = parsed_data

        self.tagdir_data["GCcontent"] = self.ignore_samples(self.tagdir_data["GCcontent"])

        if len(self.tagdir_data["GCcontent"]) > 0:
            self.add_section(
                name="Per Sequence GC Content",
                anchor="homer-tag-directory-gc-content-section",
                description="This plot shows the distribution of GC content.",
                plot=self.gc_content_plot(),
            )

    def parse_re_dist(self):
        """parses and plots restriction distribution files"""
        # Find and parse homer restriction distribution reports
        for f in self.find_log_files("homer/RestrictionDistribution", filehandles=True):
            s_name = os.path.basename(f["root"])
            s_name = self.clean_s_name(s_name, f)
            parsed_data = self.parse_restriction_dist(f)
            if parsed_data is not None:
                if s_name in self.tagdir_data["restriction"]:
                    log.debug(f"Duplicate Restriction Distribution sample log found! Overwriting: {s_name}")

                self.add_data_source(f, s_name, section="restriction")
                self.tagdir_data["restriction"][s_name] = parsed_data
                self.tagdir_data["restriction_norm"][s_name] = self.normalize(parsed_data)

        self.tagdir_data["restriction"] = self.ignore_samples(self.tagdir_data["restriction"])
        self.tagdir_data["restriction_norm"] = self.ignore_samples(self.tagdir_data["restriction_norm"])

        if len(self.tagdir_data["restriction"]) > 0:
            self.add_section(
                name="Restriction Site Tag Dist",
                anchor="homer-petag-restriction-dist-section",
                description="This plot shows the distribution of tags around restriction enzyme cut sites.",
                helptext="""Hi-C data often involves the digestion of DNA using a restriction enzyme.
                    A good quality control for the experiment is the centering of reads around the
                    restriction enzyme cut site.""",
                plot=self.restriction_dist_chart(),
            )

    def parse_tag_length_dist(self):
        """parses and plots tag length distribution files"""
        # Find and parse homer tag length distribution reports
        for f in self.find_log_files("homer/LengthDistribution", filehandles=True):
            s_name = os.path.basename(f["root"])
            s_name = self.clean_s_name(s_name, f)
            parsed_data = self.parse_length_dist(f)
            if parsed_data is not None:
                if s_name in self.tagdir_data["length"]:
                    log.debug(f"Duplicate Length Distribution sample log found! Overwriting: {s_name}")
                self.add_data_source(f, s_name, section="length")
                self.tagdir_data["length"][s_name] = parsed_data

        self.tagdir_data["length"] = self.ignore_samples(self.tagdir_data["length"])
        if len(self.tagdir_data["length"]) > 0:
            self.add_section(
                name="Tag Length Distribution",
                anchor="homer-tag-length-dist-section",
                description="This plot shows the distribution of tag length.",
                helptext="This is a good quality control for tag length inputed into Homer.",
                plot=self.length_dist_chart(),
            )

    def parse_tagInfo_data(self):
        """parses and plots taginfo files"""
        # Find and parse homer taginfo reports
        for f in self.find_log_files("homer/tagInfo", filehandles=True):
            s_name = os.path.basename(f["root"])
            s_name = self.clean_s_name(s_name, f)
            parsed_data = self.parse_tag_info_chrs(f)
            if parsed_data is not None:
                if s_name in self.tagdir_data["taginfo_total"]:
                    log.debug(f"Duplicate tag info sample log found! Overwriting: {s_name}")
                self.add_data_source(f, s_name, section="taginfo")
                self.tagdir_data["taginfo_total"][s_name] = parsed_data[0]
                self.tagdir_data["taginfo_total_norm"][s_name] = self.normalize(parsed_data[0])
                self.tagdir_data["taginfo_uniq"][s_name] = parsed_data[1]
                self.tagdir_data["taginfo_uniq_norm"][s_name] = self.normalize(parsed_data[1])

        for f in self.find_log_files("homer/tagInfo", filehandles=True):
            s_name = os.path.basename(f["root"])
            s_name = self.clean_s_name(s_name, f)
            ## collected tag_info data for general stats table and store under 'header'
            parsed_data = self.parse_tag_info(f)
            if parsed_data is not None:
                self.tagdir_data["header"][s_name] = parsed_data

        self.tagdir_data["taginfo_total"] = self.ignore_samples(self.tagdir_data["taginfo_total"])
        self.tagdir_data["taginfo_total_norm"] = self.ignore_samples(self.tagdir_data["taginfo_total_norm"])
        self.tagdir_data["taginfo_uniq"] = self.ignore_samples(self.tagdir_data["taginfo_uniq"])
        self.tagdir_data["taginfo_uniq_norm"] = self.ignore_samples(self.tagdir_data["taginfo_uniq_norm"])
        self.tagdir_data["header"] = self.ignore_samples(self.tagdir_data["header"])

        if len(self.tagdir_data["taginfo_total"]) > 0:
            self.add_section(
                name="Chromosomal Coverage",
                anchor="homer-tag-info-dist-section",
                description="This plot shows the distribution of tags along chromosomes.",
                helptext="""This is a good quality control for tag distribution and
                        could be a good indication of large duplications or deletions.""",
                plot=self.tag_info_chart(),
            )

    def parse_freq_distribution_data(self):
        """parses and plots taginfo files"""
        # Find and parse homer tag FreqDistribution_1000 reports
        for f in self.find_log_files("homer/FreqDistribution", filehandles=True):
            s_name = os.path.basename(f["root"])
            s_name = self.clean_s_name(s_name, f)
            parsed_data = self.parse_FreqDist(f)
            if parsed_data is not None:
                if s_name in self.tagdir_data["FreqDistribution"]:
                    log.debug(f"Duplicate Freq Distribution sample log found! Overwriting: {s_name}")

                self.add_data_source(f, s_name, section="FreqDistribution")
                self.tagdir_data["FreqDistribution"][s_name] = parsed_data

        self.tagdir_data["FreqDistribution"] = self.ignore_samples(self.tagdir_data["FreqDistribution"])

        if len(self.tagdir_data["FreqDistribution"]) > 0:
            self.add_section(
                name="Frequency Distribution",
                anchor="homer-freq-distribution-section",
                description="This plot shows the distribution of distance between PE tags.",
                helptext="""It is expected the the frequency of PE tags decays with
                    increasing distance between the PE tags. This plot gives an idea
                     of the proportion of short-range versus long-range interactions.""",
                plot=self.freq_dist_chart(),
            )

    def homer_stats_table_tagInfo(self):
        """Add core HOMER stats to the general stats table from tagInfo file"""

        if len(self.tagdir_data["header"]) == 0:
            return None

        headers = {
            "UniqPositions": {
                "title": "Uniq Pos",
                "description": "Numer of Unique Di-Tags Passed Through HOMER",
                "format": "{:,.0f}",
                "modify": lambda x: x * 0.000001,
                "suffix": "M",
            },
            "TotalPositions": {
                "title": "Total Pos",
                "description": "Numer of Total Di-Tags Passed Through HOMER",
                "format": "{:,.0f}",
                "modify": lambda x: x * 0.000001,
                "suffix": "M",
            },
            "fragmentLengthEstimate": {
                "title": "fragment Length",
                "description": "Estimate of Fragnment Length",
                "format": "{:,.0f}",
            },
            "peakSizeEstimate": {
                "title": "Peak Size",
                "description": "Estimate of Peak Size",
                "format": "{:,.0f}",
            },
            "tagsPerBP": {
                "title": "tagsPerBP",
                "description": "average tags Per basepair",
                "format": "{:,.3f}",
            },
            "TagsPerPosition": {
                "title": "averageTagsPerPosition",
                "description": "Average Tags Per Position",
                "format": "{:,.2f}",
            },
            "averageTagLength": {"title": "TagLength", "description": "Average Tag Length", "format": "{:,.0f}"},
            "averageFragmentGCcontent": {
                "title": "GCcontent",
                "description": "Average Fragment GC content",
                "max": 1,
                "min": 0,
                "format": "{:,.2f}",
            },
        }
        self.general_stats_addcols(self.tagdir_data["header"], headers)

    def homer_stats_table_interchr(self):
        """Add core HOMER stats to the general stats table from FrequencyDistribution file"""

        headers = {
            "InterChr": {
                "title": "InterChr",
                "description": "Fraction of Reads forming inter chromosomal interactions",
                "format": "{:,.4f}",
            }
        }
        self.general_stats_addcols(self.tagdir_data["FreqDistribution"], headers, "InterChr")

    def normalize(self, mydict, target=100):
        raw = sum(mydict.values())
        factor = target / raw
        return {key: value * factor for key, value in mydict.items()}

    def parse_twoCol_file(self, f):
        """Parse HOMER tagdirectory GCcontent file."""
        parsed_data = dict()
        firstline = True
        for line in f["f"]:
            if firstline:  # skip first line
                firstline = False
                continue
            s = line.split("\t")
            if len(s) > 1:
                k = float(s[0].strip())
                v = float(s[2].strip())
                parsed_data[k] = v

        return parsed_data

    def parse_restriction_dist(self, f):
        """Parse HOMER tagdirectory petagRestrictionDistribution file."""
        parsed_data = dict()
        firstline = True
        for line in f["f"]:
            if firstline:  # skip first line
                firstline = False
                continue
            s = line.split("\t")
            if len(s) > 1:
                nuc = float(s[0].strip())
                v1 = float(s[1].strip())
                v2 = float(s[2].strip())
                v = v1 + v2
                # parsed_data.update({nuc:v1})
                # parsed_data.update({nuc:v2})
                parsed_data.update({nuc: v})
        return parsed_data

    def parse_length_dist(self, f):
        """Parse HOMER tagdirectory tagLengthDistribution file."""
        parsed_data = dict()
        firstline = True
        for line in f["f"]:
            if firstline:  # skip first line
                firstline = False
                continue
            s = line.split("\t")
            if len(s) > 1:
                k = float(s[0].strip())
                v = float(s[1].strip())
                parsed_data[k] = v

        return parsed_data

    def parse_tag_info(self, f):
        """Parse HOMER tagdirectory taginfo.txt file to extract statistics in the first 11 lines."""
        # General Stats Table
        tag_info = dict()
        for line in f["f"]:
            s = line.split("=")
            if len(s) > 1:
                if s[0].strip() == "genome":
                    ss = s[1].split("\t")
                    if len(ss) > 2:
                        tag_info["genome"] = ss[0].strip()
                        try:
                            tag_info["UniqPositions"] = float(ss[1].strip())
                            tag_info["TotalPositions"] = float(ss[2].strip())
                        except Exception:
                            tag_info["UniqPositions"] = ss[1].strip()
                            tag_info["TotalPositions"] = ss[2].strip()
                try:
                    tag_info[s[0].strip()] = float(s[1].strip())
                except ValueError:
                    tag_info[s[0].strip()] = s[1].strip()
        return tag_info

    def parse_tag_info_chrs(self, f, convChr=True):
        """Parse HOMER tagdirectory taginfo.txt file to extract chromosome coverage."""
        parsed_data_total = {}
        parsed_data_uniq = {}
        remove = ["hap", "random", "chrUn", "cmd", "EBV", "GL", "NT_"]
        for line in f["f"]:
            s = line.split("\t")
            key = s[0].strip()
            # skip header
            if "=" in line or len(s) != 3:
                continue
            if convChr:
                if any(x in key for x in remove):
                    continue
            try:
                vT = float(s[1].strip())
                vU = float(s[2].strip())
            except ValueError:
                continue

            parsed_data_total[key] = vT
            parsed_data_uniq[key] = vU

        return [parsed_data_total, parsed_data_uniq]

    def parse_FreqDist(self, f):
        """Parse HOMER tagdirectory petag.FreqDistribution_1000 file."""
        parsed_data = dict()
        firstline = True
        for line in f["f"]:
            if firstline:
                firstline = False
                continue
            else:
                s = line.split("\t")
                if len(s) > 1:
                    k = s[0].strip()
                    if k.startswith("More than "):
                        k = re.sub("More than ", "", k)

                    k = float(k)
                    v = float(s[1].strip())
                    parsed_data[k] = v
        return parsed_data

    def parse_FreqDist_interChr(self, f):
        """Parse HOMER tagdirectory petag.FreqDistribution_1000 file to get inter-chromosomal interactions."""
        parsed_data = dict()
        firstline = True
        for line in f["f"]:
            if firstline:
                firstline = False
                interChr = float(re.sub(r"\)", "", line.split(":")[1]))
            else:
                break
        parsed_data["interChr"] = interChr
        return parsed_data

    def restriction_dist_chart(self):
        """Make the petagRestrictionDistribution plot"""

        pconfig = {
            "id": "homer-petag-restriction-dist",
            "title": "HOMER: Restriction Distribution",
            "ylab": "Reads",
            "xlab": "Distance from cut site (bp)",
            "tt_label": "<b>{point.x} bp</b>: {point.y} reads",
            "data_labels": [{"name": "Number of Tags"}, {"name": "Percenatge"}],
        }
        datasets = [self.tagdir_data["restriction"], self.tagdir_data["restriction_norm"]]

        return linegraph.plot(datasets, pconfig)

    def length_dist_chart(self):
        """Make the tagLengthDistribution plot"""

        pconfig = {
            "id": "homer-tag-length-dist",
            "cpswitch": True,
            "title": "HOMER: Tag Length Distribution",
            "ylab": "Fraction of Tags",
            "xlab": "Tag Length (bp)",
            "tt_label": "<b>{point.x} bp</b>: {point.y}",
        }
        return linegraph.plot(self.tagdir_data["length"], pconfig)

    def gc_content_plot(self):
        """Create the HTML for the Homer GC content plot"""

        pconfig = {
            "id": "homer-tag-directory-gc-content",
            "title": "HOMER: Tag Directory Per Sequence GC Content",
            "smooth_points": 200,
            "smooth_points_sumcounts": False,
            "ylab": "Normalized Count",
            "xlab": "% GC",
            "ymin": 0,
            "xmax": 1,
            "xmin": 0,
            "y_decimals": True,
            "tt_label": "<b>{point.x}% GC</b>: {point.y}",
        }
        return linegraph.plot(self.tagdir_data["GCcontent"], pconfig)

    def tag_info_chart(self):
        """Make the taginfo.txt plot"""

        ## TODO: human chrs on hg19. How will this work with GRCh genome or other, non human, genomes?
        # nice if they are ordered by size
        ucsc = ["chr" + str(i) for i in range(1, 23)].append(["chrX", "chrY", "chrM"])
        ensembl = list(range(1, 23)).append(["X", "Y", "MT"])
        pconfig = {
            "id": "homer-tag-info-dist",
            "title": "HOMER: Tag Info Distribution",
            "ylab": "Tags",
            "cpswitch_counts_label": "Number of Tags",
        }

        ## check if chromosomes starts with "chr" (UCSC) or "#" (ensembl)
        sample1 = next(iter(self.tagdir_data["taginfo_total"]))
        chrFormat = next(iter(self.tagdir_data["taginfo_total"][sample1]))

        if "chr" in chrFormat:
            chrs = ucsc
        else:
            chrs = ensembl

        return bargraph.plot(self.tagdir_data["taginfo_total"], chrs, pconfig)

    def freq_dist_chart(self):
        """Make the petag.FreqDistribution_1000 plot"""
        # Take a log of the data before plotting so that we can
        # reduce the number of points to plot evenly
        pdata = {}
        for idx, s_name in enumerate(self.tagdir_data["FreqDistribution"]):
            pdata[s_name] = {}
            for x, y in self.tagdir_data["FreqDistribution"][s_name].items():
                try:
                    pdata[s_name][math.log(float(x))] = y
                except ValueError:
                    pass
        pconfig = {
            "id": "homer-freq-distribution",
            "title": "HOMER: Frequency Distribution",
            "ylab": "Fraction of Reads",
            "xlab": "Log10(Distance between regions)",
            "smooth_points": 500,
            "smooth_points_sumcounts": False,
            "ylog": True,
        }
        return linegraph.plot(pdata, pconfig)
