Begin

  • 使用Python处理DNA序列，本质上就是 IO操作和 字符串处理。
  • 代码使用菜单和用户进行交互

获取DNA序列

在https://www.ncbi.nlm.nih.gov/可以下载

处理操作

生成DNA互补序列

本质上是CG, AT的互换

生成DNA反向序列

reverse字符串即可

生成DNA反向互补序列

在互补的基础下reverse

检测GC含量

GC字符占字符串长度的比例

DNA转录为RNA

T换为U即可

运行

可测试使用的DNA序列 

GAGTAGTCCCTTCGCAAGCCCTCATTTCACCAGGCCCCCGGCTTGGGGCGCCTTCCTTCCCCATGGCGGG
ACACCTGGCTTCGGATTTCGCCTTCTCGCCCCCTCCAGGTGGTGGAGGTGATGGGCCAGGGGGGCCGGAG
CCGGGCTGGGTTGATCCTCGGACCTGGCTAAGCTTCCAAGGCCCTCCTGGAGGGCCAGGAATCGGGCCGG
GGGTTGGGCCAGGCTCTGAGGTGTGGGGGATTCCCCCATGCCCCCCGCCGTATGAGTTCTGTGGGGGGAT
GGCGTACTGTGGGCCCCAGGTTGGAGTGGGGCTAGTGCCCCAAGGCGGCTTGGAGACCTCTCAGCCTGAG
GGCGAAGCAGGAGTCGGGGTGGAGAGCAACTCCGATGGGGCCTCCCCGGAGCCCTGCACCGTCACCCCTG
GTGCCGTGAAGCTGGAGAAGGAGAAGCTGGAGCAAAACCCGGAGGAGGCAAGTGAGCTTCGACGGGGTTG
GGGTGTGGGGAGGTGGTCATGACAGGGCAGCCTGATGGGGAAGTGGTCACCTGCAGCTGCCCAGACCTGG
CACCCAGGAGAGGAGCAGGCAGGGTCAGCTGCCCTGGCCAGGGAGGGGTGTGTATCAACTGCTGGCAGCC
CTGGCAGGCAGGGGCCAGGTGGGAAGTGGAAGCTGGATTTCGAAGAGACAACTGCCGGTGAGGGCAGAGC
AGCCTGGGAGAGTCGGAAGCTGGCCCAGGCTGGCCTTTGCTCTGGCCCAGCCCTTGTCAGGGTCTCTCAC
ATCTCCTAGGCCTGCCCAGGGTCTGGTCACTCATTACTGGCCCAGCACCAGACCCAGCTTGGGGTTGGTT
TGAGCCCCTTTTCCCACCCTTAGTCCTGCTTGAAAATTTGACCCTTATCAGACCCAAGATTTTGGCCTTA
GGGTTAAGCATAGCCTGAGGGTAAAAACAGTGCTCATTCCAGGATTATTGTTCCTGAAAGTCTAGGGTGT
GACTCGTTTCTGATAGGATCTCCTGTTTGGGCTGTGTGTGTGCGCGTTGTGAGCTGGGTTTACCTCCAGT
CAAGTATAGGGCTTGTCTTCCCCGGATCTCTGCCTCAGGCCAATGACTGGCCACTGTGTTAAGGTGCACA
CCCTGGCACCCCTTGTAGAAAGCTGGATTTTGATTGACTTCAGCCTCAGTTCCAAAGTTGTAAACAAGAA
AAATGGTGAGAGATTTCTCCAGGCCATTTGCAAATATAGAGCTGCTGCGGGATTGAAGGCATCCAGCCCT
GCTGAGGACTATTAAAGATGTATCTTCCAGTCCTTCAAGGCGACAAGTGTAAGCAATTAGAGATTAAATA
CTAAGCCTTGAGACCTCACAGAAAGGTGTGACTGGTTTCTGGAGTGACCGAGAAGCCCCAACCTCTTCGC
AGGAGGTCACTGCTGAGCCTTGAATGATAATGGCTGGCAATTGTGGTCCACTTCCTAAGTGCCTGGCTGT
GTGCTCCGTTTATACATCATTATCTCATTAACCAGCACAAAATCTCCTAGGGGGAGGTATTATTATCCTA
TTTAACGGGTTTTAACTGCTAAATGATGAAGCGAGGATTTGGACCAGTGTTTATTCCAAAACCCCAAAAC
AGAATTTGGAAAATCCAAGATAGCAGAGGGCATTTATCAGTTTGAGTTATTGGCTGAGCAGAAGTTGGGG
ATGAAAACAGCCTATTTGAAATTGATATGATCAAGCACCATTGAAACACTTCCTTGAGGCTTCAGAACTA
CAAAAAGGCCTTGTTTTTTTCTCACTAGCTGTGCACCTCTGTCTGCCGGCAGCCTCATATGGCATGCCCC
AGGGCTCAGTCCTTCAACCTCTGCTCTATCTACCCTTCCTTCCTCTCACCCACCCTCAAGGCTTAAATGC
CATTTAGACACCAGATGACTACCGCGTTTTCTGTCTCTTGTGATGGCTCCCTGAACTGCTCCACCCTGAT
CACCCAGTTGCTCAAGGCCAAACCCAGTCATCCTCAGTTTCTTTCATGTCCTACATCCTATCCTTAAGAA
ACATCCTGAATCAATCACAACCTAACCCTGGCCTCAGCCACCATCATCTCTGCTGGGATTACCGCAGTAG
CTTCTCAAATTATACTGCTTCCTCCCTACTGTCTGTGGCCAACACGTCAACTAGAGTCAGTGTTTTAAAA
GGTGTGGCCAGGCACTTTGGGAGGCCGAGGCAGGCGAATCACCTGAGGTCGGGAGTTCGAGTCCAGCCTG
ACCAACATGGCGAAACCCCATCTCTACTAAAAATACAAAATTAGCTGGGCGTGGTGACGCATGCCTGTAA
TCTCAGCTACTCAGGAAGCTGAGGCAGGAGAATCGCTTGAACCTGGGAGATGGAGGTTGCGGTGAGCCGA
GATCGCGCCAGTGCACTCCAGCCTAGGCAACAAAAGCGAAACTCTCAAAAAAAAAAAAAAAAAAGGTGAG
GCTAGGTGCGGTGGTTCACACCTGTAATCCCAGCACTTTGGGAGGCCAAGGTGGACAGATCACTTGAGGT
CTCCTGACCAGCCTGGCCAACATGGTGAAACCCCATATCTACTAAAAATACAAAAATTAGCCGGGCATGG
TGGTGGGTGCCTGTAGTCCCAGCTACTCAGGCGGCTGAGGCAGAATAGCTTGAACCCAGAAGGCGGAGAT
TGCAGTGAGCCAAGATCACGCCACAGCACTCCAGCCTGGGCGATAGAACGAGATTCCGTCTTGGTGGGGA
GAAAAAGGGTGAGAGATCATTTCGCTTGGACTAAAACAAAGTCACTATGTCTGCAACAGGATCTACCTAG
CCACCAGACCAGCTTTGGGCTCTGGAAGGCCCACTTCAGGGCCTTGCCACATTAGACTCTTGTCCTTTGC
TCAAACAATCACCTTCTCTGTCTTTAAAAGTGTCACCCTCCTCCATAATCTCCTTCCCTCCTTTACCCTA
CTCCTATAGACTGCTTTATTTTTTTTTTAATTTTTGAGATGGAGTCTCACTCTGTCCCTCAGGCTGGAGT
GCAGTGGTGCGATCTTGGCTCACTGCAAACTCCACCTCCTAGGTTCAAGCAATTCTCCTGCCTCAGCCTC
CTGAGTAGCTGGGATTATAGGGGAGCGCCATGATGCCCAGCTAATTTTTGTATTTTTAGTAGAGACAGAG
TCTCACTATGTTGACCAGGCTAGTCTTGAACTCCTGACCTCAAGTGATCTACCCACCTTGGCCTCCCAAA
GTGAAGGGATTACAGGCATGACCACTGCGCCCAGACTGCTTTACTTTTTTCCATAATATATATATATATT
TTAAATAGAGGCAGCAGGGGTGGGAGAAGGGGCGGCACGGGTCTCACTATGTTACCCAGGCTGCTTTCTA
ACTCTTGGGCTCAAGCAGTCTGCCCACCTTGGCCTCCCAAAGTGCTAGGATTTACAGACATGAGCCACTG
TGCCTGGCCATTTTTTATTTTATTTACTTTTTTATTTTTCAGAGCAGGAGTGGAAGTTTATTATTAAAAA
GTTATAGGGCAGGGAAAAAAGGAAAGTGCACTTGGAAGAGATCCAAGTGGGCAACTTGAAGAACAAGTGC
CAAATAGCACTTCTGTCATGCTGGATGTCAGGGCTCTTTGTCCACTTTGTATAGCCGCTGGCTTATAGAA
GGTGCTCGATAAATCTCTTGAATTTAAAAATCAATTAGGATGCCTCTATAGTGAAAAAGATACAGTAAAG
ATGAGGGATAATCAATTTAAAAAATGAGTAAGTACACACAAAGCACTTTATCCATTCTTATGACACCTGT
TACTTTTTTGCTGTGTTTGTGTGTATGCATGCCATGTTATAGTTTGTGGGACCCTCAAAGCAAGCTGGGG
AGAGTATATACTGAATTTAGCTTCTGAGACATGATGCTCTTCCTTTTTAATTAACCCAGAACTTAGCAGC
TTATCTATTTCTCTAATCTCAAAACATCCTTAAACTGGGGGTGATACTTGAGTGAGAGAATTTTGCAGGT
ATTAAATGAACTATCTTCTTTTTTTTTTTTCTTTGAGACAGAGTCTTGCTCTGTCACCCAGGCTGGAGTG
CAGTGGCGTGATCTCAGCTCACTGCAACCTCCGCCTCCCGGGTTCAAGTGATTCTCCTGCCTCAGCCTCC
TGAGTAGCTGGGATTACAGGTGCGTGCCACCGTGCCCAGCTAATTTTTGTGTTTTTAGTAGAGACGGGGT
TTCACCATGTTGGCCATGCTGGTCTTGAACTCCTGACCTCGTGATCTGCCCACCTCGGCCTCCCAAAGTG
CTGGAATTATAGGCGTGAGCCACCGCGCCCAGCAAAGAACTTCTAACCTTCATAACCTGACAGGTGTTCT
CGAGGCCAGGGTCTCTCTTTCTGTCCTTTCACGATGCTCTGCATCCCTTGGATGTGCCAGTTTCTGGGGG
AAGAGTAGTCCTTTGTTACATGCATGAGTCAGTGAACAGGGAATGGGTGAATGACATTTGTGGGTAGGTT
ATTTCTAGAAGTTAGGTGGGCAGCTTGGAAGGCAGAGGCACTTCTACAGACTATTCCTTGGGGCCACACG
TAGGTTCTTGAATCCCGAATGGAAAGGGGAGATTGATAACTGGTGTGTTTATGTTCTTACAAGTCTTCTG
CCTTTTAAAATCCAGTCCCAGGACATCAAAGCTCTGCAGAAAGAACTCGAGCAATTTGCCAAGCTCCTGA
AGCAGAAGAGGATCACCCTGGGATATACACAGGCCGATGTGGGGCTCACCCTGGGGGTTCTATTTGGTGG
GTTCCCCTCTGCAGATTCTGACCGCATCTCCCCTCTAAGGAGTATCCCTGAACCTAGTGGGGAGGGGCAG
GGGCAGACTACCCTCACCCATGAAGAGGAGTAGGGAGAGGGAGAAGATGCTTTGAGCTCCCTCTGGGAAG
AGGTGGTAAGCTTGGATCTCAGGGTCACAAGGGCCCTGCGTGCTCCCTCACTTTGCTTCTCTTTTGACTG
GCCTCCCCCAGGGAAGGTATTCAGCCAAACGACCATCTGCCGCTTTGAGGCTCTGCAGCTTAGCTTCAAG
AACATGTGTAAGCTGCGGCCCTTGCTGCAGAAGTGGGTGGAGGAAGCTGACAACAATGAAAATCTTCAGG
AGGTAAGGGTGGGAGGGGGATACCCGGGGACCTTCCCTTTCTTGGCCTAATTTCCATTGCTTCCATCACT
GGCTCGTAGCTCTCCGTCTTTGGTGCAGTGGTTCTCAGTGGGATGGAGTGAAATTCCTCAGTTCTGCTGG
GATAAGGTCCAGAGCCAACCCTTCCAGGATCCTGCCTTTTCACACCACCACCTGGCTCTGCTGACACATC
TAGTCACAGACCCCTGTGATGCTGTTACTCAGCAAGTCCAAAGCTTGCCCTTGTCACCCCCTTCCCACCT
GCACAGATATGCAAAGCAGAAACCCTCGTGCAGGCCCGAAAGAGAAAGCGAACCAGTATCGAGAACCGAG
TGAGAGGCAACCTGGAGAATTTGTTCCTGCAGTGCCCGAAACCCACACTGCAGCAGATCAGCCACATCGC
CCAGCAGCTTGGGCTCGAGAAGGATGTGAGTGCCATGTCTCTCTGCGGGCTCCATCTCTTTCCCCTGTCA
CCACCTCGCTTTCCCTAGCTCTGGCTCCTCCAACTGCTCTAGGGCTGTTGGCTTTGGACAGAATGTCCAA
GCAGTCAGGCCTGTCTCAGCTCATTCTCTAATGTCCTCCTCTAACTGCTCTAGGGCTGTTGGCTTTGGAT
AGAATGTCCAAGCAGAGTCAGGCCCGTCTCAGCTCATTGTCTAATGTCATTCTCCTTTCTGTCATTCACT
TGCAGGTGGTCCGAGTGTGGTTCTGTAACCGGCGCCAGAAGGGCAAGCGATCAAGCAGCGACTATGCACA
ACGAGAGGATTTTGAGGCTGCTGGGTCTCCTTTCTCAGGGGGACCAGTGTCCTTTCCTCTGGCCCCAGGG
CCCCATTTTGGTACCCCAGGCTATGGGAGCCCTCACTTCACTGCACTGTACTCCTCGGTCCCTTTCCCTG
AGGGGGAAGCCTTTCCCCCTGTCTCCGTCACCACTCTGGGCTCTCCCATGCATTCAAACTGAGGTGCCTG
CCCTTCTAGGAATGGGGGACAGGGGGAGGGGAGGAGCTAGGGAAAGAAAACCTGGAGTTTGTGCCAGGGT
TTTTGGGATTAAGTTCTTCATTCACTAAGGAAGGAATTGGGAACACAAAGGGTGGGGGCAGGGGAGTTTG
GGGCAACTGGTTGGAGGGAAGGTGAAGTTCAATGATGCTCTTGATTTTAATCCCACATCATGTATCACTT
TTTTCTTAAATAAAGAAGCCTGGGACACAGTAGATAGACACACTTA

代码

import sys
import os

DNA = ""

class toDO():
    # 判断是否导入DNA
    def isExistDNA(self):
        if DNA == "null" or DNA == "":
            print("========================================")
            print("请先导入DNA再执行操作！")
            print("========================================")
            return False
        else:
            return True

    # 7. 将DNA全部转为大写
    def toUpper(self):
        global DNA
        if not (toDO.isExistDNA(self)):
            return
        DNA = DNA.upper()
        # 写入文件
        exportFile = "upperDNA.txt"
        fp = open(exportFile, "w")
        fp.write(DNA)
        print("========================================")
        print("转换为大写的序列保存在" + exportFile + "请查看~")
        print("========================================")

    # 6. 清除程序产生的所有文件
    def cleanFiles(self):
        try:
            if os.path.exists("compDNA.txt"):
                os.remove("compDNA.txt")
            if os.path.exists("recDNA.txt"):
                os.remove("recDNA.txt")
            if os.path.exists("rev_compDNA.txt"):
                os.remove("rev_compDNA.txt")
            if os.path.exists("toRNA.txt"):
                os.remove("toRNA.txt")
            if os.path.exists("upperDNA.txt"):
                os.remove("upperDNA.txt")
        except Exception as e:
            print(e)
        print("========================================")
        print("已删除程序生成的所有文件！")
        print("========================================")

    # 0. 导入需要处理的DNA序列(请先选择此选项)
    def selectDNA(self):
        global DNA
        DNA = "null"
        # fileName = "dna.txt"
        fileName = input("请输入要读取的文件名(确保在当前目录下)：")
        if os.path.exists(fileName):
            f = open(fileName)
            DNA = f.read()
            print("========================================")
            print("导入成功！请进行后续操作~")
            print("========================================")
        else:
            print("请输入正确的文件名！")
            toDO.selectDNA(self)

    # 1. 生成DNA互补序列
    def compDNA(self):
        if not (toDO.isExistDNA(self)):
            return
          
        compDNA = ""
        tmpList = {'C': 'G', 'G': 'C', 'T': 'A', 'A': 'T',
                   'c': 'g', 'g': 'c', 't': 'a', 'a': 't'}
        for c in DNA:
            # 处理字符串中的换行符
            if (c != "\n"):
                compDNA += tmpList[c]
            else:
                compDNA += c
        # 写入文件
        exportFile = "compDNA.txt"
        fp = open(exportFile, "w")
        fp.write(compDNA)
        print("========================================")
        print("生成的序列已保存至" + exportFile + "请查看~")
        print("========================================")

    # 2. 生成DNA反向序列
    def revDNA(self):
        if not (toDO.isExistDNA(self)):
            return
          
        tmp = list(DNA)
        tmp.reverse()
        # list转为str
        recDNA = "".join(tmp)
        # print(recDNA)
        # 写入文件
        exportFile = "recDNA.txt"
        fp = open(exportFile, "w")
        fp.write(recDNA)
        print("========================================")
        print("生成的序列已保存至" + exportFile + "请查看~")
        print("========================================")

    # 3. 生成DNA反向互补序列
    def rev_compDNA(self):
        if not (toDO.isExistDNA(self)):
            return

        # 处理反向
        tmp = list(DNA)
        tmp.reverse()
        # list转为str
        recDNA = "".join(tmp)

        # 处理互补
        rev_compDNA = ""
        tmpList = {'C': 'G', 'G': 'C', 'T': 'A', 'A': 'T',
                   'c': 'g', 'g': 'c', 't': 'a', 'a': 't'}
        for c in recDNA:
            # 处理字符串中的换行符
            if (c != "\n"):
                rev_compDNA += tmpList[c]
            else:
                rev_compDNA += c

        # 写入文件
        exportFile = "rev_compDNA.txt"
        fp = open(exportFile, "w")
        fp.write(rev_compDNA)
        print("========================================")
        print("生成的序列已保存至" + exportFile + "请查看~")
        print("========================================")

    # 4. 检测GC含量
    def calGC(self):
        if not (toDO.isExistDNA(self)):
            return

        gc = DNA.count('G') + DNA.count('C') + DNA.count('g') + DNA.count('c')
        result = gc / len(DNA)
        print("========================================")
        print("当前DNA的GC含量为：" + str(result))
        print("========================================")

    # 5. DNA翻译为RNA
    def toRNA(self):
        if not (toDO.isExistDNA(self)):
            return

        rna = DNA.replace("T", "U").replace("t", "u")
        # 写入文件
        exportFile = "toRNA.txt"
        fp = open(exportFile, "w")
        fp.write(rna)
        print("========================================")
        print("生成的序列已保存至" + exportFile + "请查看~")
        print("========================================")
        # print(rna)

    # 6. 退出程序
    def quit(self):
        print("\n欢迎再次使用~\n")
        sys.exit(0)


class ProgramMenu():

    # 显示菜单界面
    def displayMenu(self):
    # 输出带颜色的文字
    # 如果不兼容的话，就输出下面不带颜色的
#         print("""
# \033[1;32;40m========================================\033[0m
# 请选择您要进行的DNA序列处理操作:

# \033[1;32;40m0. 导入需要处理的DNA序列(请先选择此选项)\033[0m
# \033[1;36;40m1. 生成DNA互补序列
# 2. 生成DNA反向序列
# 3. 生成DNA反向互补序列
# 4. 检测GC含量
# 5. DNA转录为RNA\033[0m

# \033[1;33;40m6. 删除程序产生的文件
# 7. 将DNA全部转为大写并保存\033[0m
# \033[1;31;40m8. 退出程序\033[0m

# \033[1;32;40m========================================\033[0m
# """ )

        print("""
========================================
请选择您要进行的DNA序列处理操作:

0. 导入需要处理的DNA序列(请先选择此选项)
1. 生成DNA互补序列
2. 生成DNA反向序列
3. 生成DNA反向互补序列
4. 检测GC含量
5. DNA转录为RNA

6. 删除程序产生的文件
7. 将DNA全部转为大写并保存
8. 退出程序

========================================
""")

    # 程序主进程
    def begin(self):
        while True:
            self.displayMenu()
            try:
                num = int(input("输入选项："))
            except Exception as e:
                print("请输入正确的选项！")
                continue
            if num == 8:
                toDO.quit(self)
            elif num == 0:
                toDO.selectDNA(self)
            elif num == 1:
                toDO.compDNA(self)
            elif num == 2:
                toDO.revDNA(self)
            elif num == 3:
                toDO.rev_compDNA(self)
            elif num == 4:
                toDO.calGC(self)
            elif num == 5:
                toDO.toRNA(self)
            elif num == 6:
                toDO.cleanFiles(self)
            elif num == 7:
                toDO.toUpper(self)

if __name__ == "__main__":
    ProgramMenu().begin()

参考链接：

版权属于：moluuser

本文链接：https://moluuser.com/archives/52/

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