#!/usr/bin/env python

__version__ = "3.07"

import os
import shutil
import re
import glob
from collections import OrderedDict
import argparse
import textwrap
import vcf


class Bruc_MLST:

    def __init__(self, read1, read2):
        self.fastq_list = []
        for read in [read1, read2]:
            if read: #append if not None
                self.fastq_list.append(read)
        self.paired = False
        if read2:
            self.paired = True
        self.sample_name = re.sub('[_.].*', '', os.path.basename(read1))

        #https://bmcmicrobiol.biomedcentral.com/articles/10.1186/1471-2180-7-34
        write_ref = open("ST1-MLST.fasta", 'w')
        print(">ST1-MLST", file=write_ref)
        print(" ", file=write_ref)
        write_ref.close()

    def find_mlst(self):

        sample_name = self.sample_name + "_mlst"
        fastq_list = self.fastq_list
        mlst_reference = "ST1-MLST.fasta"
        ref = re.sub('.fasta', '', os.path.basename(mlst_reference))
        os.system("samtools faidx {}  2> /dev/null" .format(mlst_reference))
        os.system("picard CreateSequenceDictionary REFERENCE={} OUTPUT={}  2> /dev/null" .format(mlst_reference, ref + ".dict"))
        os.system("bwa index {}  2> /dev/null" .format(mlst_reference))
        samfile_mlst = sample_name + ".sam"
        print(f'### {sample_name} BWA Aligning reads for Brucella MLST...')
        if self.paired:
            os.system(f'bwa mem -M -R "@RG\\tID:{sample_name}\\tSM:{sample_name}\\tPL:ILLUMINA\\tPI:250" -t 8 {mlst_reference} {fastq_list[0]} {fastq_list[1]} > {samfile_mlst}')
        else:
            os.system(f'bwa mem -M -R "@RG\\tID:{sample_name}\\tSM:{sample_name}\\tPL:ILLUMINA\\tPI:250" -t 8 {mlst_reference} {fastq_list[0]} > {samfile_mlst}')
        print(f'{sample_name} finding MLST type...')
        all_bam_mlst = sample_name + "_all.bam"
        os.system("picard AddOrReplaceReadGroups INPUT={} OUTPUT={} RGLB=lib1 RGPU=unit1 RGSM={} RGPL=illumina  2> /dev/null" .format(samfile_mlst, all_bam_mlst, sample_name))
        mapbam = sample_name + "_mapped.bam"
        os.system("samtools view -h -F4 -b -T {} {} -o {} 2> /dev/null" .format(mlst_reference, all_bam_mlst, mapbam))
        sortedbam = sample_name + "_sorted.bam"
        os.system("samtools sort {} -o {} 2> /dev/null" .format(mapbam, sortedbam))
        os.system("samtools index {} 2> /dev/null" .format(sortedbam))
        unfiltered_vcf_mlst = sample_name + "_unfiltered_mlst" + ".vcf"
        mapq_fix = sample_name + "_mapq_fix_mlst.vcf"
        vcf_mlst = sample_name + ".vcf"
        os.system("freebayes -E -1 -f {} {} > {}" .format(mlst_reference, sortedbam, unfiltered_vcf_mlst))
        # "fix" MQ notation in VCF to match GATK output
        write_fix = open(mapq_fix, 'w+')
        with open(unfiltered_vcf_mlst, 'r') as unfiltered:
            for line in unfiltered:
                line = line.strip()
                new_line = re.sub(r';MQM=', r';MQ=', line)
                print(new_line, file=write_fix)
            write_fix.close()
        # remove clearly poor positions
        os.system(r'vcffilter -f "QUAL > 20" %s > %s' % (mapq_fix, vcf_mlst))
        pos_call_dict = {}
        vcf_reader = vcf.Reader(open(vcf_mlst, 'r'))
        for record in vcf_reader:
            if record.ALT[0]:
                pos_call_dict.update({record.POS: str(record.ALT[0])})

        # Position 1629 was too close to the end of glk sequence.  Reads would not assemble properly to call possilbe SNP, therefore 100 bases of the gene were added.  Because of this all positions beyond this point are 100 more.  Same with position 1645 and 2693.

        target_pos_ref = {231: 'C', 297: 'T', 363: 'C', 398: 'C', 429: 'C', 523: 'G', 631: 'G', 730: 'G', 1247: 'G', 1296: 'C', 1342: 'G', 1381: 'A', 1648: 'C', 1685: 'C', 1741: 'C', 1754: 'G', 2165: 'A', 2224: 'T', 2227: 'C', 2297: 'G', 2300: 'A', 2344: 'A', 2352: 'G', 2403: 'C', 2530: 'G', 2557: 'G', 2578: 'G', 2629: 'A', 3045: 'A', 3054: 'G', 3118: 'G', 3295: 'C', 3328: 'C', 3388: 'A', 3966: 'C', 3969: 'G', 4167: 'G', 4271: 'C', 4296: 'G', 4893: 'C', 4996: 'G', 4998: 'T', 5058: 'G', 5248: 'A', 5672: 'G', 5737: 'C', 5928: 'A', 5963: 'G', 5984: 'C', 5987: 'C', 6025: 'G', 6045: 'G', 6498: 'G', 6499: 'C', 6572: 'A', 6627: 'T', 6715: 'C', 6735: 'T', 6745: 'G', 6785: 'T', 6810: 'C', 6828: 'C', 6845: 'C', 6864: 'G', 6875: 'C', 7382: 'G', 7432: 'G', 7464: 'G', 7594: 'G', 7660: 'T', 7756: 'A'}

        #pos_call_dict will replace target_pos_ref
        for key, value in pos_call_dict.items():
            if key in target_pos_ref.keys():
                target_pos_ref[key] = value
        ordered_combined_dict = OrderedDict(sorted(target_pos_ref.items()))
        combined_value_list = list(ordered_combined_dict.values())
        mlst_join = ''.join(combined_value_list)

        mlst_dictionary = {}
        mlst_dictionary["CTCCCGGGGCGACCCGATCGAAGCGGGAAGGCCACGGCGCGTGAGCAGCCGGGCATCTGTCCCGCGGGGTA"] = "MLST type 01"
        mlst_dictionary["CTCCCGGGGCGACCCGAGCGAAGCGGGAAGGCCACGGCGCGTGAGCAGCCGGGCATCTGTCCCGCGGGGTA"] = "MLST type 02"
        mlst_dictionary["CTCCCGTGGCGACCCGAGCGAAGCGGGAAGGCCACGGCGCGTGAGCAGCCGGGCATCTGTCCCGCGGGGTA"] = "MLST type 03"
        mlst_dictionary["CTCCCGGGGCGACCCGAGCGAAGCGGGAAGGCCAAGGCGCGTGAGCAGCCGGGCATCTGTCCCGCGGGGTA"] = "MLST type 04"
        mlst_dictionary["CTCCCGGGGCGACCCGATCGAAGCGGGAAGGCCACGGCGAGTGAGCAGCCGGGCATCTGTCCCGCGGGGTA"] = "MLST type 05"
        mlst_dictionary["TTCCTGGGGCAACCCGAGCGAGGCAGGGAGGCCGCGGCTCGTGAGCGGTCGGGCATCTGTCCCGCGGGGTA"] = "MLST type 06"
        mlst_dictionary["CTTCCTGGCCGAGCCGAGTGAAGGGGGGAGGCCACGGCGCGTGCTCGGCTGGGTACCTGTCTCGCGGTGCT"] = "MLST type 07"
        mlst_dictionary["CTTCCTGGCCGACCCGAGTGAAGGGGGGAGGCCACGGCGCGTGCGCGGCTGGGTACCCGTCTCGCGGTGCT"] = "MLST type 08"
        mlst_dictionary["CTTCCTGGCCGACCCGAGTGAAGGGGGGAGGCCACGGCGCGTGCGCGGCTGGGTACCTGTCTCGTGGTGCT"] = "MLST type 09"
        mlst_dictionary["CTTCCTGGCCGACCCGAGTGAAGGGGGGGGGCCACGGCGCGTGCTCGGCTGGGTACCTGTCTCGCGGTGCT"] = "MLST type 10"
        mlst_dictionary["CTTCCTGGCCGACCCGAGTGAAGGGGGGAGGCCACGGCGCGTGCGCGGCTGGGTACCTGTCTCGCGGTGCT"] = "MLST type 11"
        mlst_dictionary["CTTCCTGGCCGACCCGAGTGAAGGGGGGAGGCCACGGCGCGTGCTCGGCTGGGTACCTGTCTCGCGGTGCT"] = "MLST type 12"
        mlst_dictionary["CCCCCGGGCCGACTCGAGCGAAGCGAAGAGGCCACGGCGCGTGAGTGACCAGGCACCTATCCCACGGGGTA"] = "MLST type 13"
        mlst_dictionary["CCCCCGGGCCGGCCCAAGCGAAGCGGGGAGGCTACAGTGCGTGAGTGGCCAGGCACCTGTCCCGCGGGGTA"] = "MLST type 14"
        mlst_dictionary["CCCCCGGGCCGACCCGGGCGAAGCGGGGAGGCTACGGTGCGTGAGTGGCCAGGCACCTGTCCCGCGAGGTA"] = "MLST type 15"
        mlst_dictionary["CCCCCGGCCCGACCCGGGCGAAGCGGGGAGGCTACGGTGCGTGAGTGGCCAGGCACCTGTCCCGCGAGGTA"] = "MLST type 16"
        mlst_dictionary["CCCCCGGGCCGGCCCAAGCGAAGCGGGGAGGCTACAATGCGTGAGTGGCCAGGCACCTGTCCCGCAGGGTA"] = "MLST type 17"
        mlst_dictionary["CCCCCGGGCCGGCCCAAGCGAAGCGGGGAGGCTACAATGCGTGAGTGGCCAGGCACCTGTCCCGCAGGCTA"] = "MLST type 18"
        mlst_dictionary["CCCCCGGGCCGACCCGAGCGAAGCGGGGAGGACACGGCGCGTGAGTGGCCAGGCACCTGTCCCGCGGGGTA"] = "MLST type 19"
        mlst_dictionary["CCCCCGGGCCGGCCCAAGCGAAGCGGGGAGGCTACAATGCGTGAGTGGCCAGGCACATGTCCCGCAGGGTA"] = "MLST type 20"
        mlst_dictionary["CCCCCGGGCCGGCCCAAGCGAAGCGGGGAGGCTACAATGCGTGAGTGGCCAGGCACATGCCCCGCAGGGTA"] = "MLST type 21"
        mlst_dictionary["CCCCCGGGCCGACCCGAGCGAGGCGGGGAGGCCACGGCGCGGGAGTGGCCAGACACCTGTCCTGCGGGGTA"] = "MLST type 22"
        mlst_dictionary["CCCCCGGGCTGACCCGAGCGAAACGGGGAAGCCACGGCGCGTAAGTGGCCAGGCACCTGTCCCGCGGGGTA"] = "MLST type 23"
        mlst_dictionary["CCCCCGGGCTGACCCGAGCGGAACGGGGAAGCCACGGCGCGTAAGTGGCCAGGCACCTGTCCCGCGGGGTA"] = "MLST type 23x"
        mlst_dictionary["CCCCCGGGCCGACCCGAGCAAAGCGGGGAGGCCACGGCGCGTAAGTGGCCAGGCACCTGTCCCGCGGGGTA"] = "MLST type 24"
        mlst_dictionary["CCCCCGGGCCGACCCGAGCGAAGCGGGGAGGCCACGGCGCGTAAGTGGCCAGGCACCTGTCCCGCGGGGTA"] = "MLST type 25"
        mlst_dictionary["CCCCCGGGCCGACCCGAGCGAAGCGGGGAGGCCACGGCGCGTAAGTGGCCAAGCACCTGTTCCGCGGGGTA"] = "MLST type 26"
        mlst_dictionary["CCCCCGGGCCGACCCGAGCGAAGCGGGGAGACCACGGCGCATAAGTGGCCAGGCACCTGTCCCGCGGGGTA"] = "MLST type 27"
        mlst_dictionary["CCCTCGGGCCGACCTGAGCGAAGCGGGGAGACCACGGCGCATAAGTGGCCAGGCTCCTGTCCCGCGGGGTA"] = "MLST type 28"

        remove_files = glob.glob('ST1-MLST*')
        for i in remove_files:
            os.remove(i)
        remove_files = glob.glob('*-mlst*')
        for i in remove_files:
            os.remove(i)
        remove_files = glob.glob('*_mlst.vcf.idx')
        for i in remove_files:
            os.remove(i)
        os.remove(unfiltered_vcf_mlst)

        write_out = open("mlst.txt", 'w')
        if mlst_join in mlst_dictionary:
            mlst_type = mlst_dictionary[mlst_join]
            print(mlst_type)
            print(mlst_type, file=write_out)
        else:
            print("NO MLST MATCH FOUND\n")
            print("NO MLST MATCH FOUND", file=write_out)
            mlst_type="No Brucella MLST type found"
        write_out.close()
        self.mlst_type = mlst_type

        os.makedirs("mlst")
        shutil.move(vcf_mlst, "mlst")
        shutil.move("mlst.txt", "mlst")
        os.remove(samfile_mlst)
        os.remove(all_bam_mlst)
        os.remove(mapbam)
        os.remove(sortedbam)
        os.remove(f'{sortedbam}.bai')
        os.remove(mapq_fix)

if __name__ == "__main__": # execute if directly access by the interpreter

    parser = argparse.ArgumentParser(prog='PROG', formatter_class=argparse.RawDescriptionHelpFormatter, description=textwrap.dedent('''\

    ---------------------------------------------------------
    Based on https://bmcmicrobiol.biomedcentral.com/articles/10.1186/1471-2180-7-34

    Brucella MLST from WGS sequence
    
    '''), epilog='''---------------------------------------------------------''')
    
    parser.add_argument('-r1', '--read1', action='store', dest='read1', required=True, help='Required: single read')
    parser.add_argument('-r2', '--read2', action='store', dest='read2', required=False, default=None, help='Optional: paired read')
    parser.add_argument('-v', '--version', action='version', version=f'{os.path.abspath(__file__)}: version {__version__}')

    args = parser.parse_args()
    read1 = args.read1
    read2 = args.read2

    mlst = Bruc_MLST(read1, read2)
    mlst.find_mlst()