# -*- encoding=utf8 -*-

"""

python pbmapper.py -i /media/changhao/Data/python_test -x /home/changhao/app/index/mm10

"""

import os

import glob

import sys

import argparse

from utility.fastqtools import merge_fastq, reverse_complementary

from utility.biopythontools import joint_barcode_splitter_trimmer_withttaa

from utility.mappingtools import bowtie2_single as bowtie2

from utility.sambamtools import sam_to_bam, bam_dedup, bam_index_generator, bam_sorted, bam_to_bigwig, bam_to_bed

# parameters

fastqc = Bowtie2 = fastx_toolbox = Cufflinks = DESeq = DEXSeq = GATK = GFold = False

# argparse arguments

parser = argparse.ArgumentParser(description='A pipeline of PB insertion data analysis. <changhao1986@outlook.com>',

formatter_class=argparse.RawTextHelpFormatter)

parser.add_argument('-i', '--input',

help = "",

required = True)

parser.add_argument('-x', '--index',

help = "genome index dir",

required = True)

# parser.add_argument('-b', '--barcode',

# help = "",

# required = True)

args = parser.parse_args()

# init

__VERSION__ = 'V0.1'

if not os.path.exists(args.input):

sys.exit('ArgumentError:\tinput must be a file path.')

# fastq file merge

R1_files=glob.glob(os.path.join(args.input,"1_or_seq/R1*.fastq.gz"))

R2_files=glob.glob(os.path.join(args.input,"1_or_seq/R2*.fastq.gz"))

merge_fastq(R1_files, os.path.join(args.input, "2_merged"),os.path.join(args.input,"2_merged/R1.fastq.gz"))

merge_fastq(R2_files, os.path.join(args.input, "2_merged"),os.path.join(args.input,"2_merged/R2.fastq.gz"))

reverse complementary

reverse_complementary(args.input,"2_merged/R2.fastq.gz", "2_merged/R2_R.fastq.gz")

join splitter trimmer with ttaa detection

joint_barcode_splitter_trimmer_withttaa(args.input, "2_merged/R1.fastq.gz", "2_merged/R2_R.fastq.gz","5_joint_spliter_trimmer_withttaa")

# bowtie2

bowtie2(args.input, "5_joint_spliter_trimmer_withttaa", "6_bowtie2", args.index)

# samtools

sam_to_bam(args.input, "6_bowtie2", "6_bowtie2")

bam_dedup(args.input, "6_bowtie2", "7_bowtie2_dedup")

bam_sorted(args.input, "7_bowtie2_dedup", "8_bowtie2_dedup_sorted")

bam_index_generator(args.input, "8_bowtie2_dedup_sorted", "8_bowtie2_dedup_sorted")

# bamCoverage

bam_to_bigwig(args.input, "8_bowtie2_dedup_sorted", "9_bigwigfile")

# generate bedfile

bam_to_bed(args.input, "8_bowtie2_dedup_sorted", "10_bedfile")

##############################################################################################

# if not os.path.exists(args.output):

# os.mkdir(args.output)

# if not os.path.exists(args.index):

# sys.exit('ArgumentError:\tindex must be a file path.')

# if not os.path.isfile(args.barcode):

# sys.exit('ArgumentError:\tbarcode must be a file.')

###############################################################################################