#!/usr/bin/env python

""" MultiQC module to parse output from Conpair """

from __future__ import print_function
import logging
import re

from multiqc.modules.base_module import BaseMultiqcModule

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

class MultiqcModule(BaseMultiqcModule):
    """
    Conpair module class.
    """

    def __init__(self):

        # Initialise the parent object
        super(MultiqcModule, self).__init__(name='Conpair', anchor='conpair',
        href='https://github.com/nygenome/Conpair',
        info="is a fast and robust method dedicated for human tumor-normal "\
             "studies to perform concordance verification, as well as "\
             "cross-individual contamination level estimation in "\
             "whole-genome and whole-exome sequencing experiments.")

        self.conpair_data = dict()

        for f in self.find_log_files('conpair/concordance'):
            self.parse_conpair_logs(f)

        for f in self.find_log_files('conpair/contamination'):
            self.parse_conpair_logs(f)

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

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

        log.info("Found {} reports".format(len(self.conpair_data)))

        # Write parsed report data to a file
        self.write_data_file(self.conpair_data, 'multiqc_conpair')

        # Basic Stats Table
        self.conpair_general_stats_table()


    def parse_conpair_logs(self, f):
        """ Go through log file looking for conpair concordance or contamination output
        One parser to rule them all. """

        conpair_regexes = {
            'concordance_concordance': r"Concordance: ([\d\.]+)%",
            'concordance_used_markers': r"Based on (\d+)/\d+ markers",
            'concordance_total_markers': r"Based on \d+/(\d+) markers",
            'concordance_marker_threshold': r"\(coverage per marker threshold : (\d+) reads\)",
            'concordance_min_mapping_quality': r"Minimum mappinq quality: (\d+)",
            'concordance_min_base_quality': r"Minimum base quality: (\d+)",
            'contamination_normal': r"Normal sample contamination level: ([\d\.]+)%",
            'contamination_tumor': r"Tumor sample contamination level: ([\d\.]+)%"
        }

        parsed_data = {}
        for k, r in conpair_regexes.items():
            match = re.search(r, f['f'])
            if match:
                parsed_data[k] = float(match.group(1))

        def _cp_type(data):
            if 'concordance_concordance' in parsed_data:
                return 'concordance'
            elif 'contamination_normal' in parsed_data:
                return 'contamination'

        if len(parsed_data) > 0:
            if f['s_name'] in self.conpair_data:
                if(_cp_type(self.conpair_data[f['s_name']]) == _cp_type(parsed_data)):
                    log.debug("Duplicate sample name found! Overwriting: {}".format(f['s_name']))
            else:
                self.conpair_data[f['s_name']] = dict()
            self.add_data_source(f, section=_cp_type(parsed_data))
            self.conpair_data[f['s_name']].update(parsed_data)


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

        headers = {}
        headers['concordance_concordance'] = {
            'title': 'Concordance',
            'max': 100,
            'min': 0,
            'suffix': '%',
            'format': '{:,.2f}',
            'scale': 'RdYlGn'
        }
        headers['contamination_normal'] = {
            'title': 'N Contamination',
            'description': 'Normal sample contamination level',
            'max': 100,
            'min': 0,
            'suffix': '%',
            'format': '{:,.3f}',
            'scale': 'RdYlBu-rev'
        }
        headers['contamination_tumor'] = {
            'title': 'T Contamination',
            'description': 'Tumor sample contamination level',
            'max': 100,
            'min': 0,
            'suffix': '%',
            'format': '{:,.3f}',
            'scale': 'RdYlBu-rev'
        }
        self.general_stats_addcols(self.conpair_data, headers)
