生信log2|从Genbank(gbk/gbff)文件中提取序列

import sys
from Bio import GenBank
from Bio import SeqIO

gbk_filename = "GCA_000299965.1_ASM29996v1_genomic.gbff"
faa_filename = "gbff_converted.faa"

input_handle = open(gbk_filename, "r")
output_handle = open(faa_filename, "w")

for seq_record in SeqIO.parse(input_handle, "genbank") :
    print("Dealing with GenBank record %s" % seq_record.id)
    for seq_feature in seq_record.features:
        if seq_feature.type == "CDS":
            assert len(seq_feature.qualifiers['translation']) == 1
            output_handle.write(">%s, from %s protein_id=%s product=%s\n%s\n" % (
                   seq_feature.qualifiers['locus_tag'][0],
                   seq_record.name,
                   seq_feature.qualifiers['protein_id'][0],
                   seq_feature.qualifiers['product'][0],
                   seq_feature.qualifiers['translation'][0]))

output_handle.close()
input_handle.close()
print("Done")

*上面由gbk文件中提取出来的信息如下图所示

包含的信息有：
1.locus_tag,
2.protein_id (可在ncbi的batch entrez中搜索的蛋白accession号）
3.蛋白质产物
4.对应序列

• 可根据需求改脚本，比如说输入的文件以及，主要用上面的seq_feature.qualifiers进行提取,添加或删减feature。

• 参考地址

原始脚本来源

CSDN