def check_selfcomp(seq: str, threshold=4) -> bool:
if type(seq) != str or type(threshold) != int:
raise TypeError
r_seq = seq[::-1]
d = {}
for i in range(threshold, len(seq) + 1):
s = []
for base in range(len(seq) - 1):
r_oligo = r_seq[base:base + i]
if len(r_oligo) != i:
break
r_c_seq = Seq.complement(r_oligo)
if r_c_seq in seq:
s.append(r_c_seq)
d[i] = s
if not d:
return False
max_key = max(d.keys())
if max_key >= 5 or len(d[max_key]) >= 5:
return True
return False
def test_complement_of_dna(self):
seq = "ATGAAACTG"
self.assertEqual("TACTTTGAC", Seq.complement(seq))
def test_complement_of_rna(self):
seq = "AUGAAACUG"
self.assertEqual("UACUUUGAC", Seq.complement(seq))
# Import the sequence from the Biopython library
from Bio.Seq import *
def complement(seq):
comp_seq=""
mapping = {'A':'T', "C":"G", "G":"C", "T":"A"}
for nucleotide in gene:
comp_seq += mapping[nucleotide]
return comp_seq;
def reverse(seq):
rev_seq = seq[::-1]
return rev_seq
if __name__ == '__main__':
gene = "TCAGACTGGTGCCGTGGTGCTCTCGCCCGATGTGACGTCGACCGCCAGCGGCGCGATGACGCCGAGGATTTCCGTGATCGTTTCGGAGGGCACGCCGGCTGCGGTCAGCGCGTCGGCCAAGTGTCCGGCGACCAGGCTGAAGTGGTGCATGGTAATTCCGCGCCCCTGATGGACTTGCTTCATCGGCGCACCGGTATAGGGCTCGGGCCCGCCAAGCGCGGCCGCGAAAAACTCCACCTGCTTGCCCTTGAGGCGGCTCATGTTCGTACCGCTGAAGAAGGCCGATAGTTGGTCATCGGCAAGCACACGAACATAGAAGTCCTCGACGACGACTTCGATGGCCTCATGCCCGCCGATCTTGTCGTAGATGCTGATCGGCTCACGTTTGCGCAAGCGTGACAGTAGTCCCATTTTTATA"
res = reverse(complement(gene))
print(res)
# Define a sequence as a DNA Seq object
seq = Seq("CCTCAGCGAGGACAGCAAGGGACTAGCC")
# The complement() method can act just like your complement() function.
complement = seq.complement()
# Similarly, we can use the reverse_complement() method.
reverse_complement = seq.reverse_complement()
# We can even use the transcribe() method to switch alphabets to RNA
RNA = seq.transcribe()
print(RNA)
def strand_match(b, strand):
if strand == '+':
return b
else:
return Seq.complement(b)
