Rosalind第22题——ros

rosalind第22题——ros"/>

Rosalind第22题——ros

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import re#引入fasta文件得到dna序列
with open("../examples/ros_bio22_SPLC.txt")as f:file = f.readlines()
fasta = {}
for line in file:line = re.sub(r'\n', "", line)m = re.match(r'^>.*', line)if m:name = m.group()fasta[name] = ''else:fasta[name] += linetable = {} # 密码子表
#RNA密码子表
codon = """UUU F      CUU L      AUU I      GUU V
UUC F      CUC L      AUC I      GUC V
UUA L      CUA L      AUA I      GUA V
UUG L      CUG L      AUG M      GUG V
UCU S      CCU P      ACU T      GCU A
UCC S      CCC P      ACC T      GCC A
UCA S      CCA P      ACA T      GCA A
UCG S      CCG P      ACG T      GCG A
UAU Y      CAU H      AAU N      GAU D
UAC Y      CAC H      AAC N      GAC D
UAA Stop   CAA Q      AAA K      GAA E
UAG Stop   CAG Q      AAG K      GAG E
UGU C      CGU R      AGU S      GGU G
UGC C      CGC R      AGC S      GGC G
UGA Stop   CGA R      AGA R      GGA G
UGG W      CGG R      AGG R      GGG G """
codon = codon.split("\n")
#将密码子表字符串转为字典
for line in codon:i = 0pattern = repile(r'(.{3} \S+)\s*(.{3} \S+)\s*(.{3} \S+)\s*(.{3} \S+)')m = pattern.match(line)while i <= 4:single = m.group(i).split(" ")table.update({single[0]: single[1]})i += 1#获取母串序列，并分别剪切两个子串，得到没有内含子的dna，再替换T成U转录得rna
seq = []
for value in fasta.values():seq.append(value)
dna = seq.pop(0)
real_dna = dna[:dna.find(seq[0])] + dna[dna.find(seq[0]) + len(seq[0]):]
real_dna = real_dna[:real_dna.find(seq[1])] + real_dna[real_dna.find(seq[1]) + len(seq[1]):]
rna = real_dna.replace('T', 'U')#翻译
i = 0
protein = ''
while i < len(rna):if table[rna[i: i+3]] == 'Stop':breakprotein += table[rna[i: i+3]]i += 3
print(protein)