Python在生物学领域的简单应用—

DNA的反向互补序列

假设我们有一串DNA序列，存在一个名为“dna.txt”的文本文档中。那么，我们该如何用Python输出它的反向序列、互补序列以及反向互补序列呢？
在这之前，我们不妨定义一个函数，用来打开并读取txt文件。我们把这个函数命名为read_seq()，这个函数的参数为我们的文件路径。需要注意的一点是，在dna.txt文件中，存在着换行符\n和回车符\r（如下图所示），而我们只需要用到代表碱基序列的大写字母。我们可以用replace()方法来替换掉它们。

最终，我们定义的read_seq()函数如下：

def read_seq(inputfile):file = open(inputfile, "r")seq = file.read()seq = seq.replace("\n", "")seq = seq.replace("\r", "")return seq

接下来，我们需要定义dna_complement()，dna_reverse()和dna_revcomp()三个函数。在定义dna_complement()函数的时候，和上面替换换行符和回车符同样的道理，我们可以用replace()方法来替换字符串中代表碱基的大写字母。而定义后两个函数明显容易得多，我们只需要让字符串反向输出就可以了。我们定义的dna_complement()，dna_reverse()和dna_revcomp()三个函数如下所示：

def dna_complement(seq):seq = seq.upper()seq = seq.replace('A', 'T')seq = seq.replace('T', 'A')seq = seq.replace('C', 'G')seq = seq.replace('G', 'C')return seq

def dna_reverse(seq):seq = seq.upper()return seq[::-1]

def dna_revcomp(seq):seq = seq.upper()return dna_complement(seq)[::-1]

完整的代码如下所示：

def dna_complement(seq):seq = seq.upper()seq = seq.replace('A', 'T')seq = seq.replace('T', 'A')seq = seq.replace('C', 'G')seq = seq.replace('G', 'C')return seqdef dna_reverse(seq):seq = seq.upper()return seq[::-1]def dna_revcomp(seq):seq = seq.upper()return dna_complement(seq)[::-1]def read_seq(inputfile):file = open(inputfile, "r")seq = file.read()seq = seq.replace("\n", "")seq = seq.replace("\r", "")return seqif __name__ == '__main__':dna = read_seq("E:\\python_pycharm\\一些Python程序练习\\DNA\\dna.txt")print(dna)                          # 原DNA序列print(dna_complement(dna))          # DNA互补序列print(dna_reverse(dna))             # DNA反向序列print(dna_revcomp(dna))             # DNA反向互补序列

输出结果如下：

GGTCAGAAAAAGCCCTCTCCATGTCTACTCACGATACATCCCTGAAAACCACTGAGGAAGTGGCTTTTCAGATCATCTTGCTTTGCCAGTTTGGGGTTGGGACTTTTGCCAATGTATTTCTCTTTGTCTATAATTTCTCTCCAATCTCGACTGGTTCTAAACAGAGGCCCAGACAAGTGATTTTAAGACACATGGCTGTGGCCAATGCCTTAACTCTCTTCCTCACTATATTTCCAAACAACATGATGACTTTTGCTCCAATTATTCCTCAAACTGACCTCAAATGTAAATTAGAATTCTTCACTCGCCTCGTGGCAAGAAGCACAAACTTGTGTTCAACTTGTGTTCTGAGTATCCATCAGTTTGTCACACTTGTTCCTGTTAATTCAGGTAAAGGAATACTCAGAGCAAGTGTCACAAACATGGCAAGTTATTCTTGTTACAGTTGTTGGTTCTTCAGTGTCTTAAATAACATCTACATTCCAATTAAGGTCACTGGTCCACAGTTAACAGACAATAACAATAACTCTAAAAGCAAGTTGTTCTGTTCCACTTCTGATTTCAGTGTAGGCATTGTCTTCTTGAGGTTTGCCCATGATGCCACATTCATGAGCATCATGGTCTGGACCAGTGTCTCCATGGTACTTCTCCTCCATAGACATTGTCAGAGAATGCAGTACATATTCACTCTCAATCAGGACCCCAGGGGCCAAGCAGAGACCACAGCAACCCATACTATCCTGATGCTGGTAGTCACATTTGTTGGCTTTTATCTTCTAAGTCTTATTTGTATCATCTTTTACACCTATTTTATATATTCTCATCATTCCCTGAGGCATTGCAATGACATTTTGGTTTCGGGTTTCCCTACAATTTCTCCTTTACTGTTGACCTTCAGAGACCCTAAGGGTCCTTGTTCTGTGTTCTTCAACTGTTGAAAGCCAGAGTCACTAAAAATGCCAAACACAGAAGACAGCTTTGCTAATACCATTAAATACTTTATTCCATAAATATGTTTTTAAAAGCTTGTATGAACAAGGTATGGTGCTCACTGCTATACTTATAAAAGAGTAAGGTTATAATCACTTGTTGATATGAAAAGATTTCTGGTTGGAATCTGATTGAAACAGTGAGTTATTCACCACCCTCCATTCTCT
CCACACAAAAACCCCACACCAACACAACACACCAAACAACCCACAAAACCACACACCAACACCCAAAACACAACAACAACCAAACCCACAAACCCCAACCCACAAAACCCAAACAAAAACACAAACACAAAAAAAACACACCAAACACCACACCAACAAAACACACCCCCACACAACACAAAAAAACACACAACCCACACCCCAAACCCAAAACACACAACCACACAAAAAAACCAAACAACAACAACACAAAACCACCAAAAAAACCACAAACACACCACAAAACAAAAAAACAAAACAACACACCCCACCACCCAACAACCACAAACAACACAACAACAACACAACACACAAACCAACACAAACACACACAACAACCACAAAAAACACCAAAACCAAAACACACACCAACACACACAAACAACCCAACAAAAACAACAAACACAACAACCAACAACACACACAAAAAAAACAACAACAAACCAAAAAACCACACACCACCACACAAAACACACAAAAACAAAAACACAAAAACCAACAACAACACAACCACAACACAAAACACACAACCCAAACACAACAACACCAAACCCCAACAACCCACAAACAACACCAACAACCACACCACCACACACACCAACCAACAACACCACCAAACACAAACACACACAAACCACAACAAAAACACACACAAACACCACCCCACCCCCCAACCACACACCACACCAACCCAAACAAACCACAACCACCAACACACAAAACAACCCAAAAAACAACAAACACAAAAAACAAACAACAAAAACACCAAAAAAAAAAAAACACAACAAACCCACACCCAAACCAAACACAAAAACCAAACCCCAAACCCAACAAAAACACCAAAACACAACACCAACACACACCCAAACCCACCAACAACACACAACAACAACACAACAAACCCACACACACAAAAAAACCCAAACACACAACACACCAAACCAAAAACCAAAAAAAACAAAAAACCAAAAAAAACAAAAAAAAACCAACAAACAACAACCAAACCACCACACACCAAAACAAAAAAAACACAAACCAAAAAAACACAACAACAAAACAAAACAAAACACCAACCAAACACAAACAAACACACACAAAAACACCACCCACCAAACACA
TCTCTTACCTCCCACCACTTATTGAGTGACAAAGTTAGTCTAAGGTTGGTCTTTAGAAAAGTATAGTTGTTCACTAATATTGGAATGAGAAAATATTCATATCGTCACTCGTGGTATGGAACAAGTATGTTCGAAAATTTTTGTATAAATACCTTATTTCATAAATTACCATAATCGTTTCGACAGAAGACACAAACCGTAAAAATCACTGAGACCGAAAGTTGTCAACTTCTTGTGTCTTGTTCCTGGGAATCCCAGAGACTTCCAGTTGTCATTTCCTCTTTAACATCCCTTTGGGCTTTGGTTTTACAGTAACGTTACGGAGTCCCTTACTACTCTTATATATTTTATCCACATTTTCTACTATGTTTATTCTGAATCTTCTATTTTCGGTTGTTTACACTGATGGTCGTAGTCCTATCATACCCAACGACACCAGAGACGAACCGGGGACCCCAGGACTAACTCTCACTTATACATGACGTAAGAGACTGTTACAGATACCTCCTCTTCATGGTACCTCTGTGACCAGGTCTGGTACTACGAGTACTTACACCGTAGTACCCGTTTGGAGTTCTTCTGTTACGGATGTGACTTTAGTCTTCACCTTGTCTTGTTGAACGAAAATCTCAATAACAATAACAGACAATTGACACCTGGTCACTGGAATTAACCTTACATCTACAATAAATTCTGTGACTTCTTGGTTGTTGACATTGTTCTTATTGAACGGTACAAACACTGTGAACGAGACTCATAAGGAAATGGACTTAATTGTCCTTGTTCACACTGTTTGACTACCTATGAGTCTTGTGTTCAACTTGTGTTCAAACACGAAGAACGGTGCTCCGCTCACTTCTTAAGATTAAATGTAAACTCCAGTCAAACTCCTTATTAACCTCGTTTTCAGTAGTACAACAAACCTTTATATCACTCCTTCTCTCAATTCCGTAACCGGTGTCGGTACACAGAATTTTAGTGAACAGACCCGGAGACAAATCTTGGTCAGCTCTAACCTCTCTTTAATATCTGTTTCTCTTTATGTAACCGTTTTCAGGGTTGGGGTTTGACCGTTTCGTTCTACTAGACTTTTCGGTGAAGGAGTCACCAAAAGTCCCTACATAGCACTCATCTGTACCTCTCCCGAAAAAGACTGG
ACACAAACCACCCACCACAAAAACACACACAAACAAACACAAACCAACCACAAAACAAAACAAAACAACAACACAAAAAAACCAAACACAAAAAAAACAAAACCACACACCACCAAACCAACAACAAACAACCAAAAAAAAACAAAAAAAACCAAAAAACAAAAAAAACCAAAAACCAAACCACACAACACACAAACCCAAAAAAACACACACACCCAAACAACACAACAACAACACACAACAACCACCCAAACCCACACACAACCACAACACAAAACCACAAAAACAACCCAAACCCCAAACCAAAAACACAAACCAAACCCACACCCAAACAACACAAAAAAAAAAAAACCACAAAAACAACAAACAAAAAACACAAACAACAAAAAACCCAACAAAACACACAACCACCAACACCAAACAAACCCAACCACACCACACACCAACCCCCCACCCCACCACAAACACACACAAAAACAACACCAAACACACACAAACACAAACCACCACAACAACCAACCACACACACCACCACACCAACAACCACAACAAACACCCAACAACCCCAAACCACAACAACACAAACCCAACACACAAAACACAACACCAACACAACAACAACCAAAAACACAAAAACAAAAACACACAAAACACACCACCACACACCAAAAAACCAAACAACAACAAAAAAAACACACACAACAACCAACAACACAAACAACAAAAACAACCCAACAAACACACACAACCACACACAAAACCAAAACCACAAAAAACACCAACAACACACACAAACACAACCAAACACACAACACAACAACAACACAACAAACACCAACAACCCACCACCCCACACAACAAAACAAAAAAACAAAACACCACACAAACACCAAAAAAACCACCAAAACACAACAACAACAAACCAAAAAAACACACCAACACACAAAACCCAAACCCCACACCCAACACACAAAAAAACACAACACACCCCCACACAAAACAACCACACCACAAACCACACAAAAAAAACACAAACACAAAAACAAACCCAAAACACCCAACCCCAAACACCCAAACCAACAACAACACAAAACCCACAACCACACACCAAAACACCCAACAAACCACACAACACAACCACACCCCAAAAACACACC

把DNA编码链转录为mRNA

我们同样通过定义函数的方式来实现DNA编码链的转录。根据生物学相关知识，我们只需要把DNA编码链的T替换成U即可得到mRNA（在此我们忽略DNA的启动子与终止子）。代码实现如下：

def transcription(seq):# 这里我们假设给定DNA序列为编码链seq = seq.upper()seq = seq.replace('T', 'U')return seqdef read_seq(inputfile):file = open(inputfile, "r")seq = file.read()seq = seq.replace("\n", "")seq = seq.replace("\r", "")return seqif __name__ == '__main__':dna = read_seq("E:\\python_pycharm\\一些Python程序练习\\DNA\\dna.txt")print(dna)                          # 原DNA序列（编码链）print(transcription(dna))           # 转录出的mRNA序列

根据DNA编码链序列或mRNA序列翻译出蛋白质序列

我们先来讨论根据DNA编码链翻译蛋白质。定义一个新函数dna_translate()。在定义函数的过程中，我们需要思考一个问题：众所周知，mRNA翻译蛋白质是从起始密码子开始翻译，到终止密码子停止翻译。如果不考虑这个问题的话很有可能会得到错误的结果。定义函数如下：

import redef dna_translate(seq):table = {'ATA': 'I', 'ATC': 'I', 'ATT': 'I', 'ATG': 'M','ACA': 'T', 'ACC': 'T', 'ACG': 'T', 'ACT': 'T','AAC': 'N', 'AAT': 'N', 'AAA': 'K', 'AAG': 'K','AGC': 'S', 'AGT': 'S', 'AGA': 'R', 'AGG': 'R','CTA': 'L', 'CTC': 'L', 'CTG': 'L', 'CTT': 'L','CCA': 'P', 'CCC': 'P', 'CCG': 'P', 'CCT': 'P','CAC': 'H', 'CAT': 'H', 'CAA': 'Q', 'CAG': 'Q','CGA': 'R', 'CGC': 'R', 'CGG': 'R', 'CGT': 'R','GTA': 'V', 'GTC': 'V', 'GTG': 'V', 'GTT': 'V','GCA': 'A', 'GCC': 'A', 'GCG': 'A', 'GCT': 'A','GAC': 'D', 'GAT': 'D', 'GAA': 'E', 'GAG': 'E','GGA': 'G', 'GGC': 'G', 'GGG': 'G', 'GGT': 'G','TCA': 'S', 'TCC': 'S', 'TCG': 'S', 'TCT': 'S','TTC': 'F', 'TTT': 'F', 'TTA': 'L', 'TTG': 'L','TAC': 'Y', 'TAT': 'Y', 'TAA': '_', 'TAG': '_','TGC': 'C', 'TGT': 'C', 'TGA': '_', 'TGG': 'W'}start_sit = re.search('ATG', seq)protein = ""for sit in range(start_sit.end() - 3, len(seq), 3):protein += table[seq[sit:sit + 3]]if table[seq[sit:sit + 3]] == '_':breakreturn protein

完整代码如下：

import redef dna_translate(seq):table = {'ATA': 'I', 'ATC': 'I', 'ATT': 'I', 'ATG': 'M','ACA': 'T', 'ACC': 'T', 'ACG': 'T', 'ACT': 'T','AAC': 'N', 'AAT': 'N', 'AAA': 'K', 'AAG': 'K','AGC': 'S', 'AGT': 'S', 'AGA': 'R', 'AGG': 'R','CTA': 'L', 'CTC': 'L', 'CTG': 'L', 'CTT': 'L','CCA': 'P', 'CCC': 'P', 'CCG': 'P', 'CCT': 'P','CAC': 'H', 'CAT': 'H', 'CAA': 'Q', 'CAG': 'Q','CGA': 'R', 'CGC': 'R', 'CGG': 'R', 'CGT': 'R','GTA': 'V', 'GTC': 'V', 'GTG': 'V', 'GTT': 'V','GCA': 'A', 'GCC': 'A', 'GCG': 'A', 'GCT': 'A','GAC': 'D', 'GAT': 'D', 'GAA': 'E', 'GAG': 'E','GGA': 'G', 'GGC': 'G', 'GGG': 'G', 'GGT': 'G','TCA': 'S', 'TCC': 'S', 'TCG': 'S', 'TCT': 'S','TTC': 'F', 'TTT': 'F', 'TTA': 'L', 'TTG': 'L','TAC': 'Y', 'TAT': 'Y', 'TAA': '_', 'TAG': '_','TGC': 'C', 'TGT': 'C', 'TGA': '_', 'TGG': 'W'}start_sit = re.search('ATG', seq)protein = ""for sit in range(start_sit.end() - 3, len(seq), 3):protein += table[seq[sit:sit + 3]]if table[seq[sit:sit + 3]] == '_':breakreturn proteindef read_seq(inputfile):file = open(inputfile, "r")seq = file.read()seq = seq.replace("\n", "")seq = seq.replace("\r", "")return seqif __name__ == '__main__':dna = read_seq("E:\\python_pycharm\\一些Python程序练习\\DNA\\dna.txt")print(dna)print(dna_translate(dna)[:-1])

在上面程序的第43行print(dna_translate(dna)[:-1])，在最后加上[:-1]的目的是“删除”掉DNA序列末尾的_（下划线）。输出结果如下：

GGTCAGAAAAAGCCCTCTCCATGTCTACTCACGATACATCCCTGAAAACCACTGAGGAAGTGGCTTTTCAGATCATCTTGCTTTGCCAGTTTGGGGTTGGGACTTTTGCCAATGTATTTCTCTTTGTCTATAATTTCTCTCCAATCTCGACTGGTTCTAAACAGAGGCCCAGACAAGTGATTTTAAGACACATGGCTGTGGCCAATGCCTTAACTCTCTTCCTCACTATATTTCCAAACAACATGATGACTTTTGCTCCAATTATTCCTCAAACTGACCTCAAATGTAAATTAGAATTCTTCACTCGCCTCGTGGCAAGAAGCACAAACTTGTGTTCAACTTGTGTTCTGAGTATCCATCAGTTTGTCACACTTGTTCCTGTTAATTCAGGTAAAGGAATACTCAGAGCAAGTGTCACAAACATGGCAAGTTATTCTTGTTACAGTTGTTGGTTCTTCAGTGTCTTAAATAACATCTACATTCCAATTAAGGTCACTGGTCCACAGTTAACAGACAATAACAATAACTCTAAAAGCAAGTTGTTCTGTTCCACTTCTGATTTCAGTGTAGGCATTGTCTTCTTGAGGTTTGCCCATGATGCCACATTCATGAGCATCATGGTCTGGACCAGTGTCTCCATGGTACTTCTCCTCCATAGACATTGTCAGAGAATGCAGTACATATTCACTCTCAATCAGGACCCCAGGGGCCAAGCAGAGACCACAGCAACCCATACTATCCTGATGCTGGTAGTCACATTTGTTGGCTTTTATCTTCTAAGTCTTATTTGTATCATCTTTTACACCTATTTTATATATTCTCATCATTCCCTGAGGCATTGCAATGACATTTTGGTTTCGGGTTTCCCTACAATTTCTCCTTTACTGTTGACCTTCAGAGACCCTAAGGGTCCTTGTTCTGTGTTCTTCAACTGTTGAAAGCCAGAGTCACTAAAAATGCCAAACACAGAAGACAGCTTTGCTAATACCATTAAATACTTTATTCCATAAATATGTTTTTAAAAGCTTGTATGAACAAGGTATGGTGCTCACTGCTATACTTATAAAAGAGTAAGGTTATAATCACTTGTTGATATGAAAAGATTTCTGGTTGGAATCTGATTGAAACAGTGAGTTATTCACCACCCTCCATTCTCT
MSTHDTSLKTTEEVAFQIILLCQFGVGTFANVFLFVYNFSPISTGSKQRPRQVILRHMAVANALTLFLTIFPNNMMTFAPIIPQTDLKCKLEFFTRLVARSTNLCSTCVLSIHQFVTLVPVNSGKGILRASVTNMASYSCYSCWFFSVLNNIYIPIKVTGPQLTDNNNNSKSKLFCSTSDFSVGIVFLRFAHDATFMSIMVWTSVSMVLLLHRHCQRMQYIFTLNQDPRGQAETTATHTILMLVVTFVGFYLLSLICIIFYTYFIYSHHSLRHCNDILVSGFPTISPLLLTFRDPKGPCSVFFNC

类似地，我们可以把上面几个程序综合一下，实现“DNA—(转录)→mRNA—(翻译)→蛋白质”的完整过程。代码如下：

import redef mrna_translate(seq):table = {'AUA': 'I', 'AUC': 'I', 'AUU': 'I', 'AUG': 'M','ACA': 'T', 'ACC': 'T', 'ACG': 'T', 'ACU': 'T','AAC': 'N', 'AAU': 'N', 'AAA': 'K', 'AAG': 'K','AGC': 'S', 'AGU': 'S', 'AGA': 'R', 'AGG': 'R','CUA': 'L', 'CUC': 'L', 'CUG': 'L', 'CUU': 'L','CCA': 'P', 'CCC': 'P', 'CCG': 'P', 'CCU': 'P','CAC': 'H', 'CAU': 'H', 'CAA': 'Q', 'CAG': 'Q','CGA': 'R', 'CGC': 'R', 'CGG': 'R', 'CGU': 'R','GUA': 'V', 'GUC': 'V', 'GUG': 'V', 'GUU': 'V','GCA': 'A', 'GCC': 'A', 'GCG': 'A', 'GCU': 'A','GAC': 'D', 'GAU': 'D', 'GAA': 'E', 'GAG': 'E','GGA': 'G', 'GGC': 'G', 'GGG': 'G', 'GGU': 'G','UCA': 'S', 'UCC': 'S', 'UCG': 'S', 'UCU': 'S','UUC': 'F', 'UUU': 'F', 'UUA': 'L', 'UUG': 'L','UAC': 'Y', 'UAU': 'Y', 'UAA': '_', 'UAG': '_','UGC': 'C', 'UGU': 'C', 'UGA': '_', 'UGG': 'W'}start_sit = re.search('AUG', seq)protein = ""for sit in range(start_sit.end() - 3, len(seq), 3):protein += table[seq[sit:sit + 3]]if table[seq[sit:sit + 3]] == '_':breakreturn proteindef transcription(seq):# 这里我们假设给定DNA序列为编码链seq = seq.upper()seq = seq.replace('T', 'U')return seqdef read_seq(inputfile):file = open(inputfile, "r")seq = file.read()seq = seq.replace("\n", "")seq = seq.replace("\r", "")return seqif __name__ == '__main__':dna = read_seq("E:\\python_pycharm\\一些Python程序练习\\DNA\\dna.txt")print(dna)                          # 原DNA序列（编码链）mrna = transcription(dna)print(mrna)                         # 转录出的mRNA序列print(mrna_translate(mrna)[:-1])    # 翻译出的蛋白质序列

写在最后

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