python--处理 fasta 和 fastq 文件

fasta文件格式：fasta 文件为一个 ID 对应一个 序列,可以是 转录本序列, 蛋白序列

'''

V350033524L1C001R00100020323/1
AAGCTGTCCCATCAATAGCTGCCGCTGAAGGGTGGGGCTGGATGGCGTAAGCTACAGCTGAAGGAAGAACGTGAGCACGAGGCACTGAGGTGATTGGCTG
V350033524L1C001R00100069491/1
AAGCTGTCCAATCAATAGCTGCCGCTGAAGGGTGGGGCTGGATGGCGTAAGCTACAGCTGAAGGAAGAACGTGAGCACGAGGCACTGAGGTGATTGGCTG
'''

读取 fasta 文件保存为字典,对应的 ID 为 key,序列为 value:

with open(r'E:/python练习文件/test.fa', 'r') as fa:
    fa_dict = {}
    for line in fa:
        # 去除末尾换行符
        line = line.replace('\n','')
        if line.startswith('>'):
            # 去除 > 号
            seq_name = line[1:]
            fa_dict[seq_name] = ''
        else:
            # 去除末尾换行符并连接多行序列
            fa_dict[seq_name] = line.replace('\n','')
   
 # 查看结果,可以看到完整的把换行的序列拼接到一起了,保存为字典格式。
print(fa_dict)
{'V350033524L1C001R00100020323/1': 'AAGCTGTCCCATCAATAGCTGCCGCTGAAGGGTGGGGCTGGATGGCGTAAGCTACAGCTGAAGGAAGAACGTGAGCACGAGGCACTGAGGTGATTGGCTG', 'V350033524L1C001R00100069491/1': 'AAGCTGTCCAATCAATAGCTGCCGCTGAAGGGTGGGGCTGGATGGCGTAAGCTACAGCTGAAGGAAGAACGTGAGCACGAGGCACTGAGGTGATTGGCTG', 'V350033524L1C001R00100073913/1': 'AAGCTGTCCTATCAATAGCTGCCGCTGAAGGGTGGGGCTGGATGGCGTAAGCTACAGCTCAAGGAAGAACGTGAGCACGAGGCACTGAGGTGATTGGCTG', 'V350033524L1C001R00100149315/1': 'AAGCTGTCCTATCAATAGCTGCCGCTGAAGGGTGGGGCTGGATGGCGTAAGCTACAGCTCAAGGAAGAACGTGAGCACGAGGCACTGAGGTGATTGGCTG', 'V350033524L1C001R00100216048/1': 'AAGCTGTCCAATCAATAGCTGCCGCTGAAGGGTGGGGCTGGATGGCGTAAGCTACAGCTCAAGGAAGAACGTGAGCACGAGGCACTGAGGTGATTGGCTG'}

计算每条序列的 GC 含量及计算每条序列长度

# 遍历字典
for name,seq in fa_dict.items():
    # 输出名称
    print(name+ '\n')

    # 计算 G,C 碱基数量
    G_base = seq.count('G')
    C_base = seq.count('C')

    # 计算含量
    G_per = G_base/len(seq)*100
    C_per = C_base/len(seq)*100
    
    #计算长度
    length = len(seq)

    # 保留小数点后两位
    G_per = round(G_per,2)
    C_per = round(C_per,2)

    # 打印输出
    print("G percent is: "+str(G_per)+  "%")
    print("G percent is: "+str(C_per)+  "%")
    print("lenth: "+str(length))
V350033524L1C001R00100020323/1

G percent is: 37.0%
G percent is: 20.0%
lenth: 100
V350033524L1C001R00100069491/1

G percent is: 37.0%
G percent is: 19.0%
lenth: 100
V350033524L1C001R00100073913/1

G percent is: 36.0%
G percent is: 20.0%
lenth: 100
V350033524L1C001R00100149315/1

G percent is: 36.0%
G percent is: 20.0%
lenth: 100
V350033524L1C001R00100216048/1

G percent is: 36.0%
G percent is: 20.0%
lenth: 100