Biopython SeqIO: AttributeError: 'str' object has no attribute 'id'

Question

我正在尝试使用 SeqIO 过滤掉序列，但出现此错误。

Traceback (most recent call last):
  File "paralog_warning_filter.py", line 61, in <module>
.
.
.
    SeqIO.write(desired_proteins, "filtered.fasta","fasta")
AttributeError: 'str' object has no attribute 'id'

我检查了其他类似的问题，但仍然无法理解我的脚本有什么问题。

这是我正在尝试的脚本的相关部分：

fh=open('lineageV_paralog_warning_genes.fasta')
for s_record in SeqIO.parse(fh,'fasta'):
    name = s_record.id
    seq = s_record.seq
    for i in paralogs_in_all:
        if name.endswith(i):
            desired_proteins=seq
            output_file=SeqIO.write(desired_proteins, "filtered.fasta","fasta")
output_file
fh.close()

我有一个单独的 paralagos_in_all 列表，这是 ID 源。当我尝试打印 name 时，它 returns 一个正确的字符串 ID 名称，格式为 >coronopifolia_tair_real-AT2G35040.1@10.

你能帮我理解我的问题吗？提前致谢。

Answer 1

试着让我们知道（无法测试您的代码）：


from Bio.SeqRecord import SeqRecord
from Bio import SeqIO
......
.......

desired_proteins = []

fh=open('lineageV_paralog_warning_genes.fasta')
for s_record in SeqIO.parse(fh,'fasta'):
    name = s_record.id
    seq = s_record.seq
    for i in paralogs_in_all:
        if name.endswith(i):
            # desired_proteins=SeqRecord( Seq(seq), id=name) ### here seq is already a Seq object see below
            desired_proteins.append(SeqRecord( seq, id=name, description="")) # description='' removes the <unknown description> that otherwise would be present 
            
            
output_file=SeqIO.write(desired_proteins, "filtered.fasta","fasta") ## don't know how to have SeqIO.write to append to file instead of re-writing all of it

fh.close()

Biopython SeqIO: AttributeError: 'str' object has no attribute 'id'

Biopython SeqIO: AttributeError: 'str' object has no attribute 'id'

python

sequence

biopython

fasta