#!/usr/bin/env python

""" MultiQC module to parse output from Flexbar """

from __future__ import print_function
from collections import OrderedDict
import logging
import re

from multiqc.plots import bargraph
from multiqc.modules.base_module import BaseMultiqcModule

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


class MultiqcModule(BaseMultiqcModule):
    def __init__(self):

        # Initialise the parent object
        super(MultiqcModule, self).__init__(
            name="Flexbar",
            anchor="flexbar",
            href="https://github.com/seqan/flexbar",
            info="is a barcode and adapter removal tool.",
        )

        # Parse logs
        self.flexbar_data = dict()
        for f in self.find_log_files("flexbar", filehandles=True):
            self.parse_flexbar(f)

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

        if len(self.flexbar_data) == 0:
            raise UserWarning

        log.info("Found {} logs".format(len(self.flexbar_data)))
        self.write_data_file(self.flexbar_data, "multiqc_flexbar")

        # Add drop rate to the general stats table
        headers = {}
        headers["removed_bases_pct"] = {
            "title": "% bp Trimmed",
            "description": "% Total Base Pairs removed",
            "max": 100,
            "min": 0,
            "suffix": "%",
            "scale": "YlOrRd",
        }
        self.general_stats_addcols(self.flexbar_data, headers)

        # Make barplot
        self.flexbar_barplot()

    def parse_flexbar(self, f):
        def _save_data(parsed_data):
            if len(parsed_data) > 0:
                # Calculate removed_bases
                if "processed_bases" in parsed_data and "remaining_bases" in parsed_data:
                    parsed_data["removed_bases"] = parsed_data["processed_bases"] - parsed_data["remaining_bases"]
                    parsed_data["removed_bases_pct"] = (
                        float(parsed_data["removed_bases"]) / float(parsed_data["processed_bases"])
                    ) * 100.0
                if s_name in self.flexbar_data:
                    log.debug("Duplicate sample name found! Overwriting: {}".format(s_name))
                self.flexbar_data[s_name] = parsed_data

        regexes = {
            "output_filename": r"Read file:\s+(.+)$",
            "processed_reads": r"Processed reads\s+(\d+)",
            "skipped_due_to_uncalled_bases": r"skipped due to uncalled bases\s+(\d+)",
            "short_prior_to_adapter_removal": r"short prior to adapter removal\s+(\d+)",
            "finally_skipped_short_reads": r"finally skipped short reads\s+(\d+)",
            "discarded_reads_overall": r"Discarded reads overall\s+(\d+)",
            "remaining_reads": r"Remaining reads\s+(\d+)",
            "processed_bases": r"Processed bases:?\s+(\d+)",
            "remaining_bases": r"Remaining bases:?\s+(\d+)",
        }
        s_name = f["s_name"]
        parsed_data = dict()
        for l in f["f"]:
            for k, r in regexes.items():
                match = re.search(r, l)
                if match:
                    if k == "output_filename":
                        s_name = self.clean_s_name(match.group(1), f["root"])
                    else:
                        parsed_data[k] = int(match.group(1))

            # End of log output. Save and reset in case of more logs.
            if "Flexbar completed" in l:
                _save_data(parsed_data)
                s_name = f["s_name"]
                parsed_data = dict()

        # Pick up any partial logs
        _save_data(parsed_data)

    def flexbar_barplot(self):
        """ Make the HighCharts HTML to plot the flexbar rates """

        # Specify the order of the different possible categories
        keys = OrderedDict()
        keys["remaining_reads"] = {"color": "#437bb1", "name": "Remaining reads"}
        keys["skipped_due_to_uncalled_bases"] = {"color": "#e63491", "name": "Skipped due to uncalled bases"}
        keys["short_prior_to_adapter_removal"] = {"color": "#b1084c", "name": "Short prior to adapter removal"}
        keys["finally_skipped_short_reads"] = {"color": "#7f0000", "name": "Finally skipped short reads"}

        # Config for the plot
        pconfig = {
            "id": "flexbar_plot",
            "title": "Flexbar: Processed Reads",
            "ylab": "# Reads",
            "cpswitch_counts_label": "Number of Reads",
            "hide_zero_cats": False,
        }

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