sequence_x_removal.py

import unittest

def frame_calc(sequence):
    modulo = len(sequence) % 3
    if modulo == 0:
        return 0
    elif modulo == 1:
        return 1
    elif modulo == 2:
        return 2

def replacer(x, rep0, rep1, rep2):
    if x == 0:
        return rep0
    elif x == 1:
        return rep1
    elif x == 2:
        return rep2


def motif_replacer(seq, rep0, rep1, rep2, restriction_site):
    mult_mx = {
        "ecor5": 6,
        "pst1": 6,
        "nco1": 6,
        "5a": 5,
        "5t": 5
    }
    multiplier = mult_mx[restriction_site]
    seq_dup = list(seq)
    to_replace = []
    def_to_replace = []
    for i, a in enumerate(seq):
        if seq[i:i+multiplier] == "x"*multiplier:
            to_replace.append((i, i+multiplier))
        
    for i, j in enumerate(to_replace):
        print(i,j)
        if i == 0:
            def_to_replace.append(j)
        else:
            ind = def_to_replace[i-1]
            print(j[0]+1, "\n", ind)
            if j[0]+1 not in range(ind[0], ind[1]):
                def_to_replace.append(j)
        # print(i, j)
    print(def_to_replace)
    for item in def_to_replace:
        frag = replacer(frame_calc(seq[:item[0]]), rep0, rep1, rep2)
        for k, v in enumerate(seq_dup[item[0]:item[1]]):
            seq_dup[int(item[0]) + int(k)] = list(frag)[k]

    return "".join(seq_dup)


class TestStringMethods(unittest.TestCase):
    def setUp(self):
        self.rep0 = "ccttgg"
        self.rep1 = "ctatgg"
        self.rep2 = "ccacgg"
        self.restriction_site = "nco1"

    # def test_sub_um_ncoi(self):
    #     seq = "TCGGGAACGACCCCGACCGGCCTGCGCGXXXXXXCCACCCCAAATTTCGGATCGGCTGCCATTACGATTCCGGGTGCAGGAATTCCGATGACCCCAGAACAGTTACAAGTGTATGCCTGGCAAAAAGAGATTGACGACCGTAACCGTCCT"
    #     seq_mod = "TCGGGAACGACCCCGACCGGCCTGCGCGCTATGGCCACCCCAAATTTCGGATCGGCTGCCATTACGATTCCGGGTGCAGGAATTCCGATGACCCCAGAACAGTTACAAGTGTATGCCTGGCAAAAAGAGATTGACGACCGTAACCGTCCT"
    #     seq_output = motif_replacer(seq.lower(), self.rep0, self.rep1, self.rep2, self.restriction_site)
    #     self.assertTrue(seq_mod.lower() == seq_output.lower())
    #
    #
    # def test_sub_dois_ncoi(self):
    #     seq = "TCGGGAACGACCCCGACCGGCCTGCGCGXXXXXXCCACCCCAAATTTCGGATCGGCTGCCATTACGATTCCGGGTGCAGGAATTCCGATGACCCCAGAACAGTTACAAGTGTATGCCTGGCAAAAAGAGATTGACGACXXXXXXCGTCCT"
    #     seq_mod = "TCGGGAACGACCCCGACCGGCCTGCGCGCTATGGCCACCCCAAATTTCGGATCGGCTGCCATTACGATTCCGGGTGCAGGAATTCCGATGACCCCAGAACAGTTACAAGTGTATGCCTGGCAAAAAGAGATTGACGACCCTTGGCGTCCT"
    #     seq_output = motif_replacer(seq.lower(), self.rep0, self.rep1, self.rep2, self.restriction_site)
    #     self.assertTrue(seq_mod.lower() == seq_output.lower())
    #
    # def test_duas_extremidades(self):
    #     seq = "XXXXXXTCGGGAACGACCCCGACCGGCCTGCGCGCCACCCCAAATTTCGGATCGGCTGCCATTACGATTCCGGGTGCAGGAATTCCGATGACCCCAGAACAGTTACAAGTGTATGCCTGGCAAAAAGAGATTGACGACCGTCCTXXXXXX"
    #     seq_mod = "CCTTGGTCGGGAACGACCCCGACCGGCCTGCGCGCCACCCCAAATTTCGGATCGGCTGCCATTACGATTCCGGGTGCAGGAATTCCGATGACCCCAGAACAGTTACAAGTGTATGCCTGGCAAAAAGAGATTGACGACCGTCCTCCTTGG"
    #     seq_output = motif_replacer(seq.lower(), self.rep0, self.rep1, self.rep2, self.restriction_site)
    #     self.assertTrue(seq_mod.lower() == seq_output.lower())
    #
    # def test_uma_extremidade(self):
    #     seq = "XXXXXXTCGGGAACGACCCCGACCGGCCTGCGCGCCACCCCAAATTTCGGATCGGCTGCCATTACGATTCCGGGTGCAGGAATTCCGATGACCCCAGAACAGTTACAAGTGTATGCCTGGCAAAAAGAGATTGACGACCGTCCT"
    #     seq_mod = "CCTTGGTCGGGAACGACCCCGACCGGCCTGCGCGCCACCCCAAATTTCGGATCGGCTGCCATTACGATTCCGGGTGCAGGAATTCCGATGACCCCAGAACAGTTACAAGTGTATGCCTGGCAAAAAGAGATTGACGACCGTCCT"
    #     seq_output = motif_replacer(seq.lower(), self.rep0, self.rep1, self.rep2, self.restriction_site)
    #     self.assertTrue(seq_mod.lower() == seq_output.lower())
    #
    def test_repeats_juntas(self):
        seq = "XXXXXXXXXXXXTCGGGAACGACCCCGACCGGCCTGCGCGCCACCCCAAATTTCGGATCGGCTGCCATTACGATTCCGGGTGCAGGAATTCCGATGACCCCAGAACAGTTACAAGTGTATGCCTGGCAAAAAGAGATTGACGACCGTCCT"
        seq_mod = "CCTTGGCCTTGGTCGGGAACGACCCCGACCGGCCTGCGCGCCACCCCAAATTTCGGATCGGCTGCCATTACGATTCCGGGTGCAGGAATTCCGATGACCCCAGAACAGTTACAAGTGTATGCCTGGCAAAAAGAGATTGACGACCGTCCT"
        import ipdb; ipdb.set_trace()
        seq_output = motif_replacer(seq.lower(), self.rep0, self.rep1, self.rep2, self.restriction_site)
        print(seq_output)
        # self.assertTrue(seq_mod.lower() == seq_output.lower())




if __name__ == '__main__':
    unittest.main()