""" MultiQC module to parse output from Trimmomatic """


import logging
import re
from collections import OrderedDict

from multiqc import config
from multiqc.modules.base_module import BaseMultiqcModule, ModuleNoSamplesFound
from multiqc.plots import bargraph

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


class MultiqcModule(BaseMultiqcModule):
    def __init__(self):
        # Initialise the parent object
        super(MultiqcModule, self).__init__(
            name="Trimmomatic",
            anchor="trimmomatic",
            href="http://www.usadellab.org/cms/?page=trimmomatic",
            info="is a flexible read trimming tool for Illumina NGS data.",
            doi="10.1093/bioinformatics/btu170",
        )

        # Parse logs
        self.trimmomatic = dict()
        for f in self.find_log_files("trimmomatic", filehandles=True):
            self.parse_trimmomatic(f)
            self.add_data_source(f)

            # 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 to strip out ignored sample names
        self.trimmomatic = self.ignore_samples(self.trimmomatic)

        if len(self.trimmomatic) == 0:
            raise ModuleNoSamplesFound

        log.info("Found {} logs".format(len(self.trimmomatic)))
        self.write_data_file(self.trimmomatic, "multiqc_trimmomatic")

        # Add drop rate to the general stats table
        headers = OrderedDict()
        headers["dropped_pct"] = {
            "title": "% Dropped",
            "description": "% Dropped reads",
            "max": 100,
            "min": 0,
            "suffix": "%",
            "scale": "OrRd",
        }
        self.general_stats_addcols(self.trimmomatic, headers)

        # Make barplot
        self.trimmomatic_barplot()

    def parse_trimmomatic(self, f):
        s_name = None
        if getattr(config, "trimmomatic", {}).get("s_name_filenames", False):
            s_name = f["s_name"]
        for l in f["f"]:
            # Get the sample name
            if s_name is None and "Trimmomatic" in l and "Started with arguments:" in l:
                # Match everything up until the first .fastq or .fq
                match = re.search("Trimmomatic[SP]E: Started with arguments:.+?(?=\.fastq|\.fq)", l)
                if match:
                    # backtrack from the end to the first space
                    s_name = match.group().split()[-1]
                    s_name = self.clean_s_name(s_name, f)
                    if s_name in self.trimmomatic:
                        log.debug("Duplicate sample name found! Overwriting: {}".format(s_name))
                else:
                    # Try looking on the next line instead, sometimes have a line break (see issue #212)
                    l = next(f["f"])
                    match = re.search(".+?(?=\.fastq|\.fq)", l)
                    if match:
                        # backtrack from the end to the first space
                        s_name = match.group().split()[-1]
                        s_name = self.clean_s_name(s_name, f)
                        if s_name in self.trimmomatic:
                            log.debug("Duplicate sample name found! Overwriting: {}".format(s_name))

            # Get single end stats
            if "Input Reads" in l and s_name is not None:
                match = re.search(
                    "Input Reads: (\d+) Surviving: (\d+) \(([\d\.,]+)%\) Dropped: (\d+) \(([\d\.,]+)%\)", l
                )
                if match:
                    self.trimmomatic[s_name] = dict()
                    self.trimmomatic[s_name]["input_reads"] = float(match.group(1))
                    self.trimmomatic[s_name]["surviving"] = float(match.group(2))
                    self.trimmomatic[s_name]["surviving_pct"] = float(match.group(3).replace(",", "."))
                    self.trimmomatic[s_name]["dropped"] = float(match.group(4))
                    self.trimmomatic[s_name]["dropped_pct"] = float(match.group(5).replace(",", "."))
                    s_name = None

            # Get paired end stats
            if "Input Read Pairs" in l and s_name is not None:
                match = re.search(
                    "Input Read Pairs: (\d+) Both Surviving: (\d+) \(([\d\.,]+)%\) Forward Only Surviving: (\d+) \(([\d\.,]+)%\) Reverse Only Surviving: (\d+) \(([\d\.,]+)%\) Dropped: (\d+) \(([\d\.,]+)%\)",
                    l,
                )
                if match:
                    self.trimmomatic[s_name] = dict()
                    self.trimmomatic[s_name]["input_read_pairs"] = float(match.group(1))
                    self.trimmomatic[s_name]["surviving"] = float(match.group(2))
                    self.trimmomatic[s_name]["surviving_pct"] = float(match.group(3).replace(",", "."))
                    self.trimmomatic[s_name]["forward_only_surviving"] = float(match.group(4))
                    self.trimmomatic[s_name]["forward_only_surviving_pct"] = float(match.group(5).replace(",", "."))
                    self.trimmomatic[s_name]["reverse_only_surviving"] = float(match.group(6))
                    self.trimmomatic[s_name]["reverse_only_surviving_pct"] = float(match.group(7).replace(",", "."))
                    self.trimmomatic[s_name]["dropped"] = float(match.group(8))
                    self.trimmomatic[s_name]["dropped_pct"] = float(match.group(9).replace(",", "."))
                    s_name = None

    def trimmomatic_barplot(self):
        """Make the HighCharts HTML to plot the trimmomatic rates"""

        # Specify the order of the different possible categories
        keys = OrderedDict()
        keys["surviving"] = {"color": "#437bb1", "name": "Surviving Reads"}
        keys["both_surviving"] = {"color": "#f7a35c", "name": "Both Surviving"}
        keys["forward_only_surviving"] = {"color": "#e63491", "name": "Forward Only Surviving"}
        keys["reverse_only_surviving"] = {"color": "#b1084c", "name": "Reverse Only Surviving"}
        keys["dropped"] = {"color": "#7f0000", "name": "Dropped"}

        # Config for the plot
        pconfig = {
            "id": "trimmomatic_plot",
            "title": "Trimmomatic: Surviving Reads",
            "ylab": "# Reads",
            "cpswitch_counts_label": "Number of Reads",
        }

        self.add_section(plot=bargraph.plot(self.trimmomatic, keys, pconfig))
