这里用到python中Biopython包完成。
步骤：
1.安装Biopython包，在anaconda prompt中使用pip install biopython或在Spyder中使用!pip install biopython安装；
2.gbk文件转核酸序列
from Bio import SeqIO
gbk_filename = "c00079_GUT_GEN...region001.gbk"#.gbk文件名
faa_filename = "c00079_GUT_GEN...region001.fna"#输出文件名
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)
output_handle.write(">%s %s\n%s\n" % (
seq_record.id,
seq_record.description,
seq_record.seq))
output_handle.close()
input_handle.close()
3.gbk文件转蛋白序列
from Bio import SeqIO
gbk_filename = "NC_005213.gbk"
faa_filename = "NC_005213_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\n%s\n" % (
seq_feature.qualifiers['locus_tag'][0],
seq_record.name,
seq_feature.qualifiers['translation'][0]))
output_handle.close()
input_handle.close()
