python-2.7 - 使用 Biopython 基于 IDS 过滤 FASTA 文件

Question

我对 python 编程非常陌生。我有包含某些植物物种的蛋白质序列的 fasta 文件。

我想根据每个序列包含的氨基酸数量来过滤它们。标准是那些>20 个氨基酸的序列。

我能够利用biopython cookbook上的资源获得超过20个的氨基酸序列。但是，当我尝试将它们写入文件时，它给了我这个 Error 。我无法解决此错误。此外，我还想在输出文件中包含每个序列的 ID。请帮我!

代码:

import Bio
from Bio import SeqIO
for s_record in SeqIO.parse('arabidopsis_thaliana_proteome.ath.tfa','fasta'):
    name = s_record.id
    seq = s_record.seq
    seqLen = len(s_record)
    if seqLen >20:
        desired_proteins=seq
        output_file=SeqIO.write(desired_proteins, "filtered.fasta","fasta")
output_file

输入文件:Arabidopsis Thaliana

>AT5G16970
MTATNKQVILKDYVSGFPTESDFDFTTTTVELRVPEGTNSVLVKNLYLSCDPYMRIRMGKPDPSTAALAQAYTPGQPIQGYGVSRIIESGHPDYKKGDLLWGIVAWEEYSVITPMTHAHFKIQHTDVPLSYYTGLLGMPGMTAYAGFYEVCSPKEGETVYVSAASGAVGQLVGQLAKMMGCYVVGSAGSKEKVDLLKTKFGFDDAFNYKEESDLTAALKRCFPNGIDIYFENVGGKMLDAVLVNMNMHGRIAVCGMISQYNLENQEGVHNLSNIIYKRIRIQGFVVSDFYDKYSKFLEFVLPHIREGKITYVEDVADGLEKAPEALVGLFHGKNVGKQVVVVARE*

>AT4G32100
MATNACKFLCLVLLFAFVTQGYGDDSYSLESLSVIQSKTGNMVENKPEWEVKVLNSSPCYFTHTTLSCVRFKSVTPIDSKVLSKSGDTCLLGNGDSIHDISFKYVWDTSFDLKVVDGYIACS*

提前谢谢你:)

Answer 1

根据此处的 BioPython 教程:

http://biopython.org/wiki/SeqIO

SeqIO.parse() 的第一个参数应该是文件句柄，而不是文件名:

from Bio import SeqIO
with open("example.fasta", "rU") as handle:
    for record in SeqIO.parse(handle, "fasta"):
        print(record.id)

这应该有效:

import Bio
from Bio import SeqIO
fh=open('arabidopsis_thaliana_proteome.ath.tfa')
for s_record in SeqIO.parse(fh,'fasta'):
    name = s_record.id
    seq = s_record.seq
    seqLen = len(s_record)
    if seqLen >20:
        desired_proteins=seq
        output_file=SeqIO.write(desired_proteins, "filtered.fasta","fasta")
output_file
fh.close()