编写python脚本,读取目的基因的genbank格式文件,并输出无回车和空行的fasta文件,命名为gene_seq.fa。 (2)截取序列的cds区,并构建名为“cds_seq.fa”的fasta文件,按照fasta格式打印输出cds区。
时间: 2024-11-13 16:40:27 浏览: 47
首先,你需要安装一些Python库来处理GenBank文件,如`biopython`,它包含了大量的生物信息学工具。下面是一个简单的示例,说明如何完成这两个任务:
```python
# 导入需要的库
from Bio import SeqIO
# 1. 读取并整理GenBank文件
def read_gb_file(input_file):
with open(input_file, "r") as gb_fh:
records = list(SeqIO.parse(gb_fh, "genbank"))
# 创建一个新的fasta文件
output_fa = "gene_seq.fa"
with open(output_fa, "w") as fa_fh:
for record in records:
seq = str(record.seq)
# 删除回车和空行
seq = seq.replace("\n", "").replace("\r", "")
fa_fh.write(f">{record.id}\n{seq}\n")
# 2. 截取cds区域并创建新的fasta文件
def extract_cds(records):
cds_output = "cds_seq.fa"
for record in records:
if "CDS" in record.features:
feature = record.features["CDS"]
start, end = feature.location.start.position, feature.location.end.position
cds_seq = record.seq[start:end]
cds_seq_str = ">{}_cds".format(record.id)
with open(cds_output, "a") as cd_fh:
cd_fh.write(cds_seq_str + "\n" + str(cds_seq) + "\n")
# 调用函数
read_gb_file("your_genbank_file.gb")
extract_cds(records)
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