genbank to fasta 核酸

from Bio import SeqIO gbk_filename = "c00079_GUT_GEN...region001.gbk" faa_filename = "c00079_GUT_GEN...region001.fna" 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()

genbank to fasta 氨基酸

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'])==1output_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()

參考官方手冊

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