tmp.py

from itertools import chain
import itertools
import numpy as np

sequence="CAGATCGCCCATATTCGTGAGCGTAACGCTGGAATAACCGCACAAAAGACTATACGGTAGCGTAACGCTGTGAAGAAAACTTATCATAGATCGCGTAACGCTGTATGTTCTACCATGCACGGTAGCGTAACAGCTGAACTTGATGTCCGAGCTAATATTCAGCCATTCTCATGAATCCGGCGCCACGCATCGAAACAGAA"
n=4
I=16
d=4

def unique(x):
    unique_list=[]
    for i in x:
        if i not in unique_list:
            unique_list.append(i)
    return unique_list

tmp=["CCGTAACTG","GTAATGTCT","CTGCTGGAA","TAACTGCAG","GGAGGTAGA","AGGCTAACC","GTAAGATGC","CGTACCGCC","TCGGTAACA","GTAACAGTA","CGTGTAGGA","GAACGCCGC","AGCTAGACC","CCTAACACT","AATGAAACC","GTATCAGCT","CGGTGAAGC","TAATCCTGG","GGCGTAAGT","GGCGGAACG","CGAACGCCT","AACGCGACA","TAACAGTCT","GCGATACGG","CGATCTGAA","TACCGCTGC","AACGCTAGT","AGCGTGACA","GGCGTACGT","AGCGCAATC","GTCGTTAAC","GTAATGATG","ATCGGAACG","GTGTAATAA","TATCTCTGT","AGCGAAGCT","CGCTGAGGA","CCTACGCTC","CGCATGAGA","CGGTACGCA","CGCAAAGCT","GTAAGCCGC","CGATAGGTC","GGCGTATCG","GTAAAGCGA","AGACGCTAA","GCTAACCGT","AGAACGCTG","CGCACGCTC","GCGTACCGT","GCGAACCAG","GGAGGTAAA","AACCTGATA","ATATATCCG","GCGTAGCGT","AGACGGTGT","TAACACCTG","AGGCGAACT","TTCATCGAT","TCAGCTAAC","CGAACCGCA","CAGGAACGC","CCTAACCGC","TTCTCGAGC","TAGATGCTG","AACGTAGAC","TACGGTAAG","GCGGTCAAC","GCGAACACA","GCGGTAACG","TAGACGGTA","AGCGGAGCG","TAACCGCAG","AACACTAGA","CAGTAAAGC","TTAACTCTG","CTATCGCTC","ATGAATCGC","CTATATGTT","CGACGCTCG","AGACGAACA","GTATCGCGC","AGCGTCATC","CGTGGAAGT","GGTAACCAT","CGCAAACGC","CCTGTAATG","GTCTAACGT","TCGTGAACA","TGATACGCT","GTATCGCGT","TAACTATGC","GCTGAGATA","AGTCGTAGA","GCCGAACGT","GCAACGGCT","AAGGTCGCG","GGAACTCTG","CGCTACGCT","TCATCGTAA","CGTAGCATC","TAAACGCGG","AGGTCAACT","TACGCATGA","GCAGAACGT","AACTGGCTG","CGTGTAATA","TAACAGCGG","TGCAGTAAC","TAACCTGTA","AGCGTAAAG","AGCTAACGC","AGCATAATC","CTGAATGTT","GAGTAACAC","CCACGAATC","CGTGATACG","AACGTGTGA","CGCATTCAC","GACGTAAAC","CGAACGTTT","GGAGGTAGG","GATAGACGT","AACGGTGAA","CGTGAAACG","GTGACGCTT","GTAACGTAC","AAGCGTATA","GCGAACAGA","TAACTGCAT","GACTAACTA","TAACGTACG","CTAACCTGG","AAACTGATC","GGAGCTATC","TAACGTCAT","AGACCGCTG","TAAAGCTTG","GGCGTAAGG","TATATCCGC","CGAGTAAGC","CGGAGCTAG","TATATCGCG","GCGTACAGA","GCGCAACTC","GTGACGCTC","CGTGTAAGG","GCGTCACAC","GAACACTGC","AACGCGGTA","TATCGGAGT","AACGCTCGT","AGAGTACGC","GTGAAAGCT","TAGTCGTGA","AGCTGTATA","AAACACTGT","TTAACTGCT","TATTCTACC","GCGTAGATC","AGATCGCTG","GCGTAAGTA","CTGTAAACG","GCGGTATAC","TAACAGGCT","GTAACAGTT","CAGTGTAGC","CTGGAACGC","GAACGTGAT","TCAACACTG","GTAAAGTGA","GCACGCTGT","AGCGAAACC","CGTCAACGC","TTACGCTGA","TATAACGCT","GCAGTATCG","CGTTAACCA","AAACGCGTG","AACGCGAGA","GCGACGCGA","CTAACGTAG","CATAACGTC","TCGAGTAAC","CGTAGTCGA","GCGTAAGAT","GCGTATAGC","TCAAACGCT","GCTGTGAAC","CATAATACG","AGCTAAGCC","GAACGCCGA","GTACGTGTA","GGTAACTAG","CGTACTGCA","CTAACGTGT","AATACACGG","ATCGGAGCT","CTAGACGCA","TAGACGGAA","ATCGTAATA","GCGTCAAGC","GAGTATCGC","TAGCGCATG","ACGATAGAC","AGATCCGGC","AGCGAGACT","TACCGCTGG","TCGGTAACC","GATGGTAAT","CCGCTAACA","GGTACGCCC","GAACGCGAA","ATGAGTCGC","CATGAACGT","GCGTACGTG","TATCGGAAC","AAGATAGCG","AACCGCTCG","AGTCGCCTA","ATACGCATG","AGTCTAACC","GTAGCCTAA","GTATCGTGC","ATACCGCTG","GCAGTACAC","AACGCTGAG","CGTGTAGTC","AGCTAAACG","TATCGCTGT","AGCTAAGCA","CGCTGAACT","CAGTACGCA","TAGACGTCT","GTAAAGCGC","TTATGCGTA","GTAACCGCT","CGAACGCTC","TATGATCTC","GTAACGTGG","AGCATTAAC","CGTGTAGGT","GTACGTGTC","AAGCGATAA","AACACTAGT","AGTCGATAA","GCAGTAGCG","ATGATCGTC","GTATCACTG","TAGACCTGC","GTAACCTTG","AACGGCTAT","GTAGCAGTA","GCGTATACG","GTAAAGATG","AAGAATCGC","GACGTAAGA","AGCTAACGG","GGAACGCTC","GAAAGCTGC","TGCGCTAAC","GTAACGCTG","CGCTAGGTA","AGACGCTCT","CGTACCTGA","AACAGGCTG","CGTGTGAGC","CTAACTCTA","GGTAAGCAG","GCGAACGAC","GTGGTAACG","CGTAGAGTC","AACAGCGTG","ACGATAGCG","CGAACCTTT","GTAACCGTG","GTACTGCTA","TAACGTGTC","GTAAAGTGC","TCAACCTGC","CTATCGCTG","GTAAAGCAT","CGATGAAGC","AGCCTAAGA","AACGATAAC","GTAACAGTG","AAGTGTAAC","TAATCGCAT","GCCTAACCG","TAATCCTGA","TAAGCTGCT","GGAGGTAAG","GCGTATATG","GTAACCGAT","GAACGTGAG","GCGAACAGT","AGCAGTAAC","GTAGCCGCT","GCGTAGCGC","CTGTAACTG","CATAACGTG","TCACCATAC","CGGAACGAT","GTACTGCTC","TCAGCGAAC","AAACTTCAT","AGCAGTATA","GTAATGCCG","CGTACACGC","TTGCGTGAA","CGCTGATAA","GATATACGC","AGCTAATCG","TGAAAGCTG","TAACGACTG","GTACCGCTA","CTAAAGCTC","TGAACGCGT","GCGTACGAT","TTTCACCAT","GGGTAACGC","ATGATCGAT","TATCCGCTG","AATCGTGTA","TGGCGTAAC","TAACGTCAG","CGATGTAAT","TACGCTGGA","AGCCGGTAA","TGTACGTAC","GTTAGCGCT","TAACCGTCT","TCAACTCTG","CTGTAACCA","GCCTAAAGC","TAACTGCGT","GCGATAAAC","GCGGAAACG","GCATAACCA","ATCGAACGC","TAAAGCATG","AGACGAACT","CGAACTCTC","ACGATGCGA","GCGGTTAAC","GCGATAATC","CGAACCGCT","AGCGAGACA","CGGAGTCGA","GGAACGCTA","GTATCGTCT","CGAACGCTT","TTAACGCTG","AATCGCTCT","CGATCAACG","GTATAAGCT","ATCGCATGT","GGACGCGTT","AGGCGAACA","CGCATGAAC","TAACGTGGT","TAAACGCTG","GTAACAGAT","ATCGTAAGC","GCTATCGCG","ATATACGCG","AGCTGAACA","GTACGCTGT","GCCGTACGT","AGACGTGTA","GTGACGCTG","GATCAGCGT","TAGGTAGCG","ATACGCTTG","AACGCTGTA","CCATAGAAT","TACCGCTGT","GTATACAGC","GCTGTATCG","AGACGCCTG","CTCTGAATG","GTAACTCTG","GGAGGCGTA","GTCAGTAAC","AACGGTATG","CCATGATCA","CGCCATGAA","GGAGCGAAG","TAACCTCGC","CCGAACGCA","TACGCTGAT","CGCACGCTT","CATAAACGC","AACGCTGAT","ATATCCGCC","TATCGGTGG","ATTCGCGAG","GAACGCTTG","CTATCGCTA","CGAGTAACG","GCGTACAGC","GTGAACGTC","GTAACGGTG","AATCTGCTG","AACGCCGCA","TTAGCCGTA","CCTAATCGC","GAGGAACGC","AGCGACACC","TCAACGATG","GTAAAGGTG","AGCGTGAAC","ACGCGATAG","AGTATCAGC","GACTAACAG","GTAATCCTG","GC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print("step1")
com=[''.join(c) for c in itertools.product('ATCG', repeat=7)]
com=list(set(com))
print("step2")
tmp_com=[]
for i in tmp:
    tmp_com2=[x+i for x in com]
    tmp_com.append(tmp_com2)
com=tmp_com

#com=unique(x=com)
# possible=["A","C","T","G"]
# com=possible
# for x in range(0,I-1):
#     tmp=[]
#     com=list(itertools.product(com, possible))
#     joined_list=[]
#     for x in com:
#         tmp = x[0]+x[1]
#         joined_list.append(tmp)
#     com=joined_list

f = open('myfile', 'w')
for x in com:
    for_com=[]
    start_point=0
    #print(x)
    while start_point <= len(sequence):
        len_through_sequence=start_point
        error=0
        len_through_x = 0
        len_of_matching_string=0
        #print(sequence[counter])
        while len_of_matching_string <= I:
            if len_of_matching_string ==0:
                if (len_through_x) >= len(x):
                    break
                elif (len_through_sequence) >= len(sequence):
                    break
                elif x[len_through_x] == sequence[len_through_sequence]:
                    len_through_sequence=len_through_sequence+1
                    len_of_matching_string=len_of_matching_string+1
                    len_through_x=len_through_x+1
                    output_list="1M"
                    start_point=len_through_sequence
                else:
                    len_through_sequence=len_through_sequence+1
            else:
                if error > d:
                    break
                elif (len_through_x) >= len(x):
                    break
                elif (len_through_sequence) >= len(sequence):
                    break
                elif x[len_through_x] == sequence[len_through_sequence]:
                    len_through_sequence=len_through_sequence+1
                    len_of_matching_string=len_of_matching_string+1
                    len_through_x=len_through_x+1
                    if output_list[-1] == "M":
                        tmp = output_list[-2:]
                        tmp= int(tmp[0])
                        tmp=tmp+1
                        tmp=str(tmp)+"M"
                        output_list=output_list[:-2]+tmp
                    else:
                        output_list=output_list+"1M"
                elif (len_of_matching_string) == I:
                    break
                else:
                    check = 0
                    for t in range(1,n+2):
                        if (len_through_sequence+t+1) > len(sequence):
                            error = d+1
                            break
                        elif (len_through_x+t+1) > len(x):
                            error = d+1
                            break
                        elif error >d:
                            break
                        elif x[len_through_x+t] == sequence[len_through_sequence]:
                            len_through_sequence=len_through_sequence+1
                            len_of_matching_string=len_of_matching_string+2
                            len_through_x=len_through_x+t+1
                            tmp=str(t)+"I1M"
                            output_list=output_list+tmp
                            error=error+t
                            check=1
                            break
                        elif x[len_through_x] == sequence[len_through_sequence+t]:
                            len_through_sequence=len_through_sequence+t+1
                            len_of_matching_string=len_of_matching_string+2
                            len_through_x=len_through_x+1
                            tmp=str(t)+"D1M"
                            output_list=output_list+tmp
                            error=error+t
                            check=1
                            break
                        elif x[len_through_x+t] == sequence[len_through_sequence+t]:
                            len_through_sequence=len_through_sequence+t+1
                            len_through_x=len_through_x+t+1
                            len_of_matching_string=len_of_matching_string+2
                            tmp=str(t)+"X1M"
                            output_list=output_list+tmp
                            error=error+t
                            check=1
                            break
                        if check == 0:
                            len_through_x=len_through_x+t+1
        if error <= d and len_of_matching_string >= I:
            for_com.append(str(start_point)+" "+output_list)
        start_point=start_point+1
    #print(len(for_com))
    if len(for_com) == n:
        f.write(x+",")#+"\n")
        #for x in for_com:
        #    f.write(str(x)+"\n")
f.close()