QAseq-Fusion_v2.1/py_script/breakpoint_stat_single_v6.3.py

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

import time,argparse
from StatReadsFusion import SingleReadsFusion as SRF

def GetHomo(homo_file,homo_dict):
    
    with open(homo_file,'r') as hf:
        for line in hf:
            info = line.strip("\n").split("\t")
            primer = info[0]
            info_list = info[1].split(",")
            homo_dict[primer]=info_list

def GetInfo(info_file,info_dict,primer_seq_dict):
    
    with open(info_file,'r') as inf:
        for line in inf:
            info = line.strip("\n").split("\t")
            primer = info[0]
            info_dict[primer]=info
            seq = info[1]
            if seq not in primer_seq_dict.keys():
                primer_seq_dict[seq]=[info[0]]
            else:
                primer_seq_dict[seq].append(info[0])

def GetUniqUMIPrimer(ID_list,readsPrimer_dict):
    UMIs_dict={}
    Primer_dict={}
    for ID in ID_list:
        temp=ID.split("_")
        if len(temp)>=5:
            UMI_tmp=ID.split("_")
            UMI = UMI_tmp[2]
            ReadsID = UMI_tmp[0]
            primer = readsPrimer_dict[ReadsID]
            UMIs_dict[UMI]=0
            Primer_dict[primer]=0
    return len(UMIs_dict),len(Primer_dict)

def main(indir,readsIDFile,homo_file,info_file):

    t1=time.time()

    homo_dict={}
    info_dict={}
    primer_seq_dict={}

    #double fuison
    fusion_file=indir+"/fusion_stat.txt"
    fusion_dict={}
    fusion_header=""
    with open(fusion_file,'r') as dff:
        fusion_header = dff.readline()
        for line in dff:
            info = line.strip("\n").split("\t")
            site = info[0]
            fusion_dict[site]=info

    #double fusion readsID
    fusion_ID_file=indir+"/fusion_readsID.txt"
    fusion_ID_dict={}
    fusion_ID_info_list=[]
    ID_header=""
    with open(fusion_ID_file,'r') as dff:
        ID_header = dff.readline()
        for line in dff:
            info = line.strip("\n").split("\t")
            site = info[0]
            readsID = info[1]
            if site not in fusion_ID_dict.keys():
                fusion_ID_dict[site]=[readsID]
            else:
                fusion_ID_dict[site].append(readsID)
            fusion_ID_info_list.append(info)

    GetHomo(homo_file,homo_dict)
    GetInfo(info_file,info_dict,primer_seq_dict)

    single_points_file=indir+"/single_breakpoint.txt"


    single_site_info_dict={}
    single_site_ID_dict={}
    single_site_total_list=[]
    readsPrimer_dict={}
    srf=SRF(homo_dict,info_dict,primer_seq_dict)
    srf.StatPrimer(readsIDFile,readsPrimer_dict)

    with open(single_points_file,'r') as spf:
        header = spf.readline().strip("\n").split("\t")
        Reads_index = header.index("ReadsID")
        Site_index = header.index("Site")
        for line in spf:
            info = line.strip("\n").split("\t")
            site = info[Site_index]
            ID = info[Reads_index]
            single_site_total_list.append(info)
            if site not in single_site_info_dict.keys():
                single_site_info_dict[site]=[info]
                single_site_ID_dict[site]=[ID]
            else:
                single_site_info_dict[site].append(info)
                single_site_ID_dict[site].append(ID)
    
    single_site_cluster_dict={}
    single_double_site_dict={}
    single_select_list=[]
    #combine seq
    for site in single_site_info_dict.keys():
        results=srf.GetSingleCombine(single_site_info_dict[site])
        if len(results[0])<10:
            continue
        single_site_cluster_dict[site]=list(results)
        for double_site in fusion_dict.keys():
            if srf.CheckSite(site,double_site):
                double_temp_list=fusion_dict[double_site]
                fusion_seq = double_temp_list[-1]
                if srf.CheckFusionSeq(results[0]+results[1],fusion_seq):
                    single_select_list.append(site)
                    if double_site not in single_double_site_dict.keys():
                        single_double_site_dict[double_site]=[site]
                    else:
                        single_double_site_dict[double_site].append(site)
    
    #将single cluster加到fusion_dict中
    for ds in single_double_site_dict.keys():
        site_list = single_double_site_dict[ds]
        temp_ID = []
        for site in site_list:
            ID_list = single_site_ID_dict[site]
            temp_ID.extend(ID_list)
            for ID_temp in ID_list:
                fusion_ID_info_list.append([ds,ID_temp,'Single'])
        singleNum = len(temp_ID)
        info = fusion_dict[ds]
        info[5] = str(singleNum)
        temp_ID.extend(fusion_ID_dict[ds])
        results=GetUniqUMIPrimer(temp_ID,readsPrimer_dict)
        UMIs = results[0]
        primerNum = results[1]
        info[6] = str(UMIs)
        info[7] = str(primerNum)
        fusion_dict[ds]=info

    #将single 加到fusion dict中
    #points ont the same front
    site_ops=[]
    for item in single_site_total_list:
        site = item[0]
        if site in single_select_list:
            continue
        mismatch_seq= item[1]
        match_seq = item[2]
        readsID = item[4]
        results=srf.GetSinglePoint(readsID,mismatch_seq,match_seq)
        if results[0] and len(results[1])>0:
            for item_list in results[1]:
                site_ops.append(site)
                #['GGCATGGTGGTGGGCGTCTGTAGTCCCAGCTACTCAGGAGGCTGAGG', 'chr10:59897395', 'chr10:59897425']
                fusion_seq=item_list[0]
                site1 = item_list[1]
                site1_e = item_list[2]
                site2 = site
                site2_e = item[3]
                singleNum = len(single_site_ID_dict[site])
                results_NUM=GetUniqUMIPrimer(single_site_ID_dict[site],readsPrimer_dict)
                UMIs = results_NUM[0]
                primerNum = results_NUM[1]
                out_str=[site1+"-"+site2,site1_e,site2_e,'0','0',str(singleNum),str(UMIs),str(primerNum),fusion_seq]
                fusion_dict[out_str[0]] = out_str
    
    #输出fusion stat final
    fusion_final_file=indir+"/fusion_stat_final.txt"
    fusion_final=open(fusion_final_file,'w')
    fusion_final.write(fusion_header)
    for site in fusion_dict.keys():
        fusion_final.write("\t".join(fusion_dict[site])+"\n")
    fusion_final.close()

    #输出fusion stat readsID
    fusion_readsID_file=indir+"/fusion_readsID_final.txt"
    fusion_readsID=open(fusion_readsID_file,'w')
    fusion_readsID.write(ID_header)
    for info in fusion_ID_info_list:
        fusion_readsID.write("\t".join(info)+"\n")
    fusion_readsID.close()

    #输出single cluster结果
    single_cluster_file=indir+"/single_stat.txt"
    single_cluster=open(single_cluster_file,'w')
    single_cluster.write("\t".join(["Point","PointDown","SingleNum","UMI","PrimerPair","MismatchSeq","MatchSeq"])+"\n")
    site_count={}
    site_out={}
    for site in single_site_cluster_dict.keys():
        if site not in site_ops:
            singleNum = len(single_site_ID_dict[site])
            results = GetUniqUMIPrimer(single_site_ID_dict[site],readsPrimer_dict)
            PointDown=single_site_info_dict[site][0][3]
            UMIs = results[0]
            primerNum = results[1]
            site_count[site] = singleNum
            info = [site,PointDown,str(singleNum),str(UMIs),str(primerNum)]
            info.extend(single_site_cluster_dict[site])
            site_out[site]=info

    site_count_sort= sorted(site_count.items(), key=lambda d:d[1], reverse = True)
    num = len(site_count_sort)
    for index in range(num):
        site = site_count_sort[index][0]
        single_cluster.write("\t".join(site_out[site])+"\n")
    single_cluster.close()

    t2=time.time()
    print("Times: "+str(int(t2-t1))+"s")
    print("BreakPoints Stat Single Done!")


if __name__ == '__main__':
    parser = argparse.ArgumentParser(description='single breakpoints primers')
    parser.add_argument('-i', required=True, type=str, help="indir")
    parser.add_argument('-r', required=True, type=str, help="reads primer file")
    parser.add_argument('-m', required=True, type=str, help="primer homo file")
    parser.add_argument('-f', required=True, type=str, help="primer info file")
    args = parser.parse_args()
    main(args.i,args.r,args.m,args.f)