Beispiel #1
0
def test_rattus():
    library = Fasta(library_path)
    queries = Fasta(query_path)

    query_sequence = str(queries["Rattus"])
    #query_sequence = str(library["sp|P06757|ADH1_RAT Alcohol dehydrogenase 1 OS=Rattus norvegicus GN=Adh1 PE=1 SV=3"])
    #query_sequence = str(library["tr|G0Z9N0|G0Z9N0_MALDO Alcohol dehydrogenase (Fragment) OS=Malus domestica GN=Adh1-1 PE=4 SV=1"])
    #query_sequence = str(library["tr|A0A0J6Z9N4|A0A0J6Z9N4_9MYCO Alcohol dehydrogenase OS=Mycobacterium obuense GN=adh_1 PE=4 SV=1"])
    #query_sequence = str(library["tr|A0A0A9PM57|A0A0A9PM57_ARUDO Adh1 OS=Arundo donax PE=4 SV=1"])
    query_sequence = str(library["tr|Q94462|Q94462_DROBU Alcohol dehydrogenase OS=Drosophila buzzatii GN=Adh1 PE=3 SV=1"])
    #query_sequence = str(library["sp|P48586|ADH1_DROMN Alcohol dehydrogenase 1 OS=Drosophila montana GN=Adh1 PE=3 SV=2"])
    #query_sequence = str(library["tr|W6S386|W6S386_9RHIZ Alcohol dehydrogenase zinc-binding domain protein OS=Rhizobium sp. LPU83 GN=adh1 PE=3 SV=1"])
    #query_sequence = str(library["tr|A0A0E9DQE5|A0A0E9DQE5_CHLTH NADP-dependent alcohol dehydrogenase OS=Chlamydia trachomatis GN=adh_1 PE=3 SV=1"])
    library_sequence = str(library["tr|Q8K571|Q8K571_RAT ADH-like protein OS=Rattus norvegicus GN=Adh1 PE=2 SV=1"])

    aligned1, aligned2, score = align(library_sequence, query_sequence)
    outline = outline_alignment_for(aligned1, aligned2)

    with open('rattus_test.txt', 'a') as fl:
        print(query_sequence, file=fl)
        print(library_sequence, file=fl)
        print(score, file=fl)
        print(aligned1, file=fl)
        print(outline,  file=fl)
        print(aligned2, file=fl)
Beispiel #2
0
def test_simple():
    #str1 = "TACCGA"
    #str2 = "ACTGAC"

    str1 = "HEAGAWGHEE"
    str2 = "PAWHEAE"

    str1 = "CCATCGCCATCG"
    str2 = "GCATCGGC"

    aligned1, aligned2, score = align(db_seq=str1, query_seq=str2)
    alignment = outline_alignment_for(aligned1, aligned2)
    print(aligned1)
    print(alignment)
    print(aligned2)
    print(score)