#!/usr/bin/env python
# -*- coding: utf-8 -*-

# 2023.10.27. v2.0: 2.0以target_location midpoint为中心，因此取消 pct 计算
# 2023.12.06. v2.1: 2.1增加 cleavage_site 推测, 修正 deletion 错位, 以 cleavage_site 为中心
# 2025.04.25. 修正大小写问题
# 2025.06.11. 调整跳过已存在的candidates的代码顺序

import os,sys,re,time
from itertools import product, permutations

if sys.version_info < (3,0):
    import platform
    raise Exception(f'python3 is needed, while running {platform.python_version()} now')

import offtracker
import offtracker.X_sequence as xseq
script_dir = os.path.abspath(os.path.dirname(offtracker.__file__))
script_folder= os.path.join(script_dir, 'utility')

import argparse
import pandas as pd
import polars as pl
import pybedtools
import multiprocessing as mp
from Bio.Blast.Applications import NcbiblastnCommandline 

def main():
    parser = argparse.ArgumentParser()
    parser.description='Generate candidate regions by sgRNA sequence'
    parser.add_argument('--sgrna' ,       type=str, required=True, help='One sgRNA sequence without PAM' )
    parser.add_argument('--pam'   ,       type=str, required=True, help='The protospacer adjacent motif' )
    parser.add_argument('--pam_location', type=str, default='downstream', help='Upstream or downstream, default is downstream (Cas9)' )
    parser.add_argument('--name'  ,       type=str, required=True, help='custom name of the sgRNA' )
    parser.add_argument('-r','--ref'    , type=str, required=True, help='The fasta file of reference genome')
    parser.add_argument('-b','--blastdb', type=str, required=True, help='blast database')
    parser.add_argument('-o','--outdir' , type=str, required=True, help='The output folder')
    parser.add_argument('-g','--genome' , type=str, default='hg38', help='File of chromosome sizes, or "hg38", "mm10" ')
    parser.add_argument('-t','--thread' , type=int, default=4,     help='Number of threads for parallel computing')
    # parser.add_argument('--quick_mode'  , action='store_true',  help='Quick mode is deprecated due to blast flaw.')

    args = parser.parse_args()
    
    
    if (args.genome == 'hg38') or (args.genome == 'mm10'):
        dir_chrom_sizes = os.path.join(script_folder, f'{args.genome}.chrom.sizes')
    else:
        dir_chrom_sizes = args.genome
    
    sgRNA_name = args.name
    sgRNA_seq  = args.sgrna
    PAM = args.pam
    PAM_loc = args.pam_location.lower()
    n_threads  = args.thread
    dir_output = args.outdir
    if not os.path.exists(dir_output):
        os.makedirs(dir_output)
    dir_ref_fa = args.ref
    blast_db   = args.blastdb
    # quick_mode = args.quick_mode
    
    # parameters for alignment
    half_width = 100
    pct_params = 1.0
    frag_len= half_width*2
    dir_df_candidate = os.path.join(dir_output, f'df_candidate_{sgRNA_name}.csv')
    if os.path.isfile(dir_df_candidate):
        print(f'{dir_df_candidate} exists, skipped.') 
        return 'skipped'
    
    sgRNA_seq = sgRNA_seq.upper()
    PAM = PAM.upper()
    dir_sgRNA_fasta = os.path.join(dir_output, f'{sgRNA_name}_PAM.fasta')
    dir_sgRNA_blast = os.path.join(dir_output, f'{sgRNA_name}_PAM.blast')
    dir_sgRNA_bed   = os.path.join(dir_output, f'{sgRNA_name}_PAM.bed')
    
    if PAM_loc == 'downstream':
        possible_sgRNA_PAM = list(product([sgRNA_seq],xseq.possible_seq(PAM)))
    elif PAM_loc == 'upstream':
        possible_sgRNA_PAM = list(product(xseq.possible_seq(PAM),[sgRNA_seq]))
    else:
        raise Exception(f'PAM_location should be "upstream" or "downstream", while {PAM_loc} is given.')
    possible_sgRNA_PAM = [''.join(combination) for combination in possible_sgRNA_PAM]
    n_seq = len(possible_sgRNA_PAM)
    
    ID = pd.Series(['seq']*n_seq) + pd.Series(range(1,n_seq+1)).astype(str)
    df_sgRNA_PAM = pd.DataFrame({'ID':ID,'sequence':possible_sgRNA_PAM})
    xseq.write_fasta(df_sgRNA_PAM, dir_sgRNA_fasta)
    
    #########
    # BLAST #
    #########
    # 2025.07.02 基于 blast 的缺陷更新

    if os.path.isfile(dir_sgRNA_blast):
        print(f'{dir_sgRNA_blast} exists, skipped.')
    else:
        blastx_cline = NcbiblastnCommandline(query=dir_sgRNA_fasta, task='blastn-short',out=dir_sgRNA_blast,
                                                db=blast_db, evalue=100000,outfmt=6, num_threads=n_threads,
                                                gapopen=4, gapextend=2, reward=2, word_size=4, dust='no', soft_masking=False)   
        print(f'BLAST for candidate off-target sites of {sgRNA_name}.')
        blastx_cline()
        print(f'BLAST finished.')
    
    ##############
    # Output bed #
    ##############
    
    # 2025.07.02 基于 blast 的缺陷更新
    len_sgRNA = len(sgRNA_seq)
    blast_regions = pl.read_csv(dir_sgRNA_blast, separator='\t',has_header=False)
    blast_regions.columns = ['query acc.','chr','% identity','alignment length','mismatches','gap opens','q. start','q. end','st','ed','evalue','bit score']

    # reverse strand
    blast_regions = blast_regions.with_columns((pl.col('st') > pl.col('ed')).cast(pl.Int8).alias('reverse'))
    blast_regions_f = blast_regions.filter(pl.col('reverse') == 0)
    blast_regions_r = blast_regions.filter(pl.col('reverse') == 1)
    blast_regions_r = blast_regions_r.with_columns([
        pl.col('ed').alias('st'),
        pl.col('st').alias('ed')
    ])
    blast_regions = pl.concat([blast_regions_f, blast_regions_r])

    # add location 
    blast_regions = blast_regions.with_columns(
        (pl.col('chr') + ':' + pl.col('st').cast(str) + '-' + pl.col('ed').cast(str)).alias('location')
    )
    # filter, sort, dedup
    blast_regions = blast_regions.with_columns(mis=(len_sgRNA - 1 - pl.col('q. end')+pl.col('q. start')+pl.col('mismatches')+pl.col('gap opens')).cast(pl.Int8))
    blast_regions = blast_regions.with_columns(mis2=(len_sgRNA - pl.col('alignment length')*pl.col('% identity')/100).round().cast(pl.Int8))
    blast_regions = blast_regions.filter((pl.col('mis')<8)|(pl.col('mis2')<8))
    blast_regions = blast_regions.sort('mis').unique('location',keep='first', maintain_order=True)
    blast_regions = blast_regions.select([
        'chr', 'st', 'ed', 'query acc.', '% identity', 'alignment length', 'mismatches',
        'gap opens', 'q. start', 'q. end', 'evalue', 'bit score', 'reverse', 'location', 'mis', 'mis2'
    ])

    # 输出 bed 用于后续 alignment score 计算
    blast_regions_bed = blast_regions.select(['chr', 'st', 'ed'])
    blast_regions_bed.write_csv(dir_sgRNA_bed, separator='\t', include_header=False)

    # 对 bed 进行排序但不合并
    a = pybedtools.BedTool(dir_sgRNA_bed)
    a.sort(g=dir_chrom_sizes).saveas( dir_sgRNA_bed )
    print(f'Output {sgRNA_name}_PAM.bed')
    
    
    ###################
    # alignment score #
    ###################

    #########
    # 读取 blast bed
    #########
    common_chr = pd.Series(['chr']*23).str[:] + pd.Series(range(23)).astype(str).str[:]
    common_chr = pd.concat([common_chr, pd.Series(['chrX','chrY'])]).to_numpy()

    bed_short = xseq.X_readbed(dir_sgRNA_bed)
    bed_short = bed_short[bed_short['chr'].isin(common_chr)].copy()
    bed_short['midpoint'] = ((bed_short['st'] + bed_short['ed'])/2).astype(int)
    bed_short['st'] = bed_short['midpoint'] - half_width
    bed_short['ed'] = bed_short['midpoint'] + half_width
    bed_short.loc[bed_short['st']<0,'st']=0
    bed_short = bed_short.drop_duplicates()

    #########
    # 根据 bed_f 位点 ed 前后 half_width 取基因组序列
    #########

    temp_bed = os.path.join(dir_output, 'temp.bed')
    xseq.write_bed(bed_short.iloc[:,:3], temp_bed)
    a = pybedtools.BedTool(temp_bed)
    fasta = pybedtools.example_filename(dir_ref_fa)
    a = a.sequence(fi=fasta)
    with open(a.seqfn) as f:
        fasta = {} 
        for line in f:
            line = line.strip() # 去除末尾换行符
            if line[0] == '>':
                header = line[1:]
            else:
                sequence = line
                fasta[header] = fasta.get(header,'') + sequence

    # pybedtools 得到位置 chrA:X-Y 时，X数字会往左多1bp

    #########
    # local alignment
    #########
    # 生成 DNA_matrix
    mismatch_score = 0.01
    base_codes = list(xseq.ambiguous_nt.keys())
    all_base_pairs = list(permutations(base_codes,2)) + [(x,x) for x in base_codes]
    DNA_matrix = {x : xseq.get_base_score(*x, mismatch_score=mismatch_score) for x in all_base_pairs}
    # 添加 PAM
    if PAM_loc == 'downstream':
        sgRNA_PAM_fw = sgRNA_seq + PAM
    else:
        sgRNA_PAM_fw = PAM + sgRNA_seq

    sgRNA_PAM_rv = xseq.reverse_complement(sgRNA_PAM_fw)

    list_args_fw=[]
    list_args_rv=[]
    for a_key, a_seq in fasta.items():
        # 2025.04.25 修正大小写问题
        a_seq = re.sub('[^ATCG]','N',a_seq.upper())
        list_args_fw.append( [a_key, sgRNA_PAM_fw, a_seq, frag_len, DNA_matrix, mismatch_score] )
        list_args_rv.append( [a_key, sgRNA_PAM_rv, a_seq, frag_len, DNA_matrix, mismatch_score] )
    st = time.time()
    with mp.Pool(n_threads) as p:
        list_align_forward = p.starmap(xseq.sgRNA_alignment, list_args_fw)
    ed = time.time()
    print('align_forward:{:.2f}'.format(ed-st))
    st = time.time()
    with mp.Pool(n_threads) as p:
        list_align_reverse = p.starmap(xseq.sgRNA_alignment, list_args_rv)
    ed = time.time()
    print('align_reverse:{:.2f}'.format(ed-st))
    #
    df_align_forward = pd.DataFrame(list_align_forward, columns= ['fw_score','fw_pct','fw_target','fw_location','fw_deletion','fw_insertion','fw_mismatch'])
    df_align_reverse = pd.DataFrame(list_align_reverse, columns= ['rv_score','rv_pct','rv_target','rv_location','rv_deletion','rv_insertion','rv_mismatch'])
    df_align_reverse['rv_target'] = df_align_reverse['rv_target'].apply(xseq.reverse_complement)
    df_candidate = pd.concat([df_align_forward,df_align_reverse],axis=1)
    df_candidate['location'] = fasta.keys()
    df_candidate['alignment_score'] = df_candidate[['fw_score','rv_score']].max(axis=1)
    #df_candidate['fw_score_2'] = df_candidate['fw_score']*(pct_params-df_candidate['fw_pct'].abs())
    #df_candidate['rv_score_2'] = df_candidate['rv_score']*(pct_params-df_candidate['rv_pct'].abs())
    #df_candidate['best_seq_score'] = df_candidate[['fw_score_2', 'rv_score_2']].max(axis=1)
    #df_candidate['best_strand'] = df_candidate[['fw_score_2', 'rv_score_2']].idxmax(axis='columns').replace({'fw_score_2':'+', 'rv_score_2':'-'})
    #df_candidate.loc[df_candidate['fw_score_2']==df_candidate['rv_score_2'],'best_strand']='equal_score'
    df_candidate['best_seq_score'] = df_candidate[['fw_score', 'rv_score']].max(axis=1)
    df_candidate['best_strand'] = df_candidate[['fw_score', 'rv_score']].idxmax(axis='columns').replace({'fw_score':'+', 'rv_score':'-'})
    df_candidate.loc[df_candidate['fw_score']==df_candidate['rv_score'],'best_strand']='equal_score'
            
    # GG check
    # 2023.12.05 增加 cleavage_site 推测
    list_best_target = []
    list_best_location = []
    list_cleavage_site = []
    list_delete = []
    list_insert = []
    list_mismat = []
    list_GG = []
    for a_row in df_candidate.iterrows():
        if a_row[1]['best_strand']=='+':
            list_best_target.append(a_row[1]['fw_target'])
            list_best_location.append(a_row[1]['fw_location'])
            list_cleavage_site.append(int(a_row[1]['fw_location'].split('-')[1]) - 6)
            list_delete.append(a_row[1]['fw_deletion'])
            list_insert.append(a_row[1]['fw_insertion'])
            list_mismat.append(a_row[1]['fw_mismatch'])
            if a_row[1]['fw_target'][-2:]=='GG':
                list_GG.append('OK')
            else:
                list_GG.append('NO')                     
        elif a_row[1]['best_strand']=='-':
            list_best_target.append(a_row[1]['rv_target'])
            list_best_location.append(a_row[1]['rv_location'])
            list_cleavage_site.append(int(a_row[1]['rv_location'].split('-')[0].split(':')[1]) + 5)
            list_delete.append(a_row[1]['rv_deletion'])
            list_insert.append(a_row[1]['rv_insertion'])
            list_mismat.append(a_row[1]['rv_mismatch'])
            if a_row[1]['rv_target'][-2:]=='GG':
                list_GG.append('OK')
            else:
                list_GG.append('NO')  
        else:
            if a_row[1]['fw_target'][-2:]=='GG':
                list_best_target.append(a_row[1]['fw_target'])
                list_best_location.append(a_row[1]['fw_location'])
                list_cleavage_site.append(int(a_row[1]['fw_location'].split('-')[1]) - 6)
                list_delete.append(a_row[1]['fw_deletion'])
                list_insert.append(a_row[1]['fw_insertion'])
                list_mismat.append(a_row[1]['fw_mismatch'])
                list_GG.append('OK_same_score')
            # 发现没有 GG 则看 RC
            elif a_row[1]['rv_target'][-2:]=='GG':
                list_best_target.append(a_row[1]['rv_target'])
                list_best_location.append(a_row[1]['rv_location'])
                list_cleavage_site.append(int(a_row[1]['rv_location'].split('-')[0].split(':')[1]) + 5)
                list_delete.append(a_row[1]['rv_deletion'])
                list_insert.append(a_row[1]['rv_insertion'])
                list_mismat.append(a_row[1]['rv_mismatch'])
                list_GG.append('OK_same_score')
            else:
                list_best_target.append(a_row[1]['fw_target'])
                list_best_location.append(a_row[1]['fw_location'])
                list_cleavage_site.append(int(a_row[1]['fw_location'].split('-')[1]) - 6)
                list_delete.append(a_row[1]['fw_deletion'])
                list_insert.append(a_row[1]['fw_insertion'])
                list_mismat.append(a_row[1]['fw_mismatch'])                    
                list_GG.append('NO_same_score')
    # 记入 df_candidate
    df_candidate['deletion'] = list_delete
    df_candidate['insertion'] = list_insert
    df_candidate['mismatch'] = list_mismat
    df_candidate['GG'] = list_GG
    df_candidate['best_target'] = list_best_target
    df_candidate['target_location'] = list_best_location
    df_candidate['cleavage_site'] = list_cleavage_site

    # 2.0 更新一下格式
    df_candidate = df_candidate.drop_duplicates(subset=['target_location']).reset_index(drop=True)
    df_candidate = pd.concat([xseq.bedfmt(df_candidate['target_location']), df_candidate],axis=1)
    # df_candidate['midpoint'] = ((df_candidate['ed'] + df_candidate['st'])/2).astype(int)
    df_candidate = xseq.add_ID(df_candidate, midpoint='cleavage_site')

    # 2025.07.02 为了削弱 blast 缺陷增加了候选位点数量，这里过滤一下减少计算
    df_candidate['mis_all'] = df_candidate[['mismatch','deletion','insertion']].sum(axis=1)
    df_candidate = df_candidate[df_candidate['mis_all']<8]

    # 2025.07.06 增加 region 标记用于去重
    # 将 df_candidate 按照染色体分组
    candidate_groups = df_candidate.groupby('chr')
    # 定义一个空的列表，用于存储每个染色体的数据
    list_dp = []
    for chr_name, chr_candidate in candidate_groups:
        dp_marked = offtracker.mark_regions_single_chr(pl.DataFrame(chr_candidate))
        list_dp.append(dp_marked)
    df_candidate = pl.concat(list_dp)

    # 改成 pl 输出
    df_candidate.write_csv(dir_df_candidate)
    print(f'Output df_candidate_{sgRNA_name}.csv')
    os.remove(temp_bed)

    return 'Done!'
    

if __name__ == '__main__' :
    result = main()
    print(result)



