使用Bio.SeqIO编写单行FASTA

Question

QIIME请求这里(这里)关于它作为输入接收的fasta文件:

The file is a FASTA file, with sequences in the single line format. That is, sequences are not broken up into multiple lines of a particular length, but instead the entire sequence occupies a single line.

Bio.SeqIO.write当然遵循格式建议,并每隔80个bps拆分序列.我可以写自己的作家来写那些"单行"的快速 - 但我的问题是,如果有一种方法,我错过了SeqIO这样做.

Answer 1

BioPython的SeqIO模块使用FastaIO子模块以FASTA格式读写.

的FastaIO.FastaWriter类可以输出不同数量的每行的字符但界面的这部分不是通过暴露SeqIO.您需要FastaIO直接使用.

所以不要使用:

from Bio import SeqIO
SeqIO.write(data, handle, format)

使用:

from Bio.SeqIO import FastaIO
fasta_out = FastaIO.FastaWriter(handle, wrap=None)
fasta_out.write_file(data)

要么

for record in data:
    fasta_out.write_record(record)