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。 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: 2024-10-26 10:16:24 浏览: 71
gb2fasta:Perl脚本,用于将GenBank记录转换为FASTA格式
编写Python脚本来处理这种任务,我们可以使用biopython库,它是一个强大的生物学计算工具包,特别是用于序列分析。以下是一个简单的示例:
```python
from Bio import SeqIO
# 读取GenBank文件
with open("your_genbank_file.gb", "r") as gb_file:
records = list(SeqIO.parse(gb_file, "genbank"))
# 创建一个空字典存储每个记录的CDS区
cds_sequences = {}
for record in records:
# 查找并提取CDS区域
for feature in record.features:
if feature.type == "CDS":
cds_start = feature.location.start.position
cds_end = feature.location.end.position
seq_id = f"{record.id}_{feature.qualifiers['locus_tag'][0]}_CDS" # 使用 locus_tag 作为标识符
seq = str(record[cds_start:cds_end])
# 添加到字典,键为ID,值为CDS序列
cds_sequences[seq_id] = seq
# 将CDS序列写入新的fasta文件
with open("cds_seq.fa", "w") as out_file:
for seq_id, seq in cds_sequences.items():
out_file.write(f">{seq_id}\n{seq}\n")
# 将整个基因序列写入另一个fasta文件,去除回车和空行
gene_seqs = [str(record.seq) for record in records]
with open("gene_seq.fa", "w") as out_file:
out_file.writelines(f">{record.id}\n{seq.strip()}\n" for record, seq in zip(records, gene_seqs))
```
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