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

Question

I am trying to filter out sequences using SeqIO but I am getting this error.

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

I checked other similar questions but still couldn't understand what is wrong with my script.

Here is the relevant part of the script I am trying:

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()

I have a separate paralagos_in_all list and that is the ID source. When I try to print name it returns a proper string id names which are in this format >coronopifolia_tair_real-AT2G35040.1@10.

Can you help me understand my problem? Thanks in advance.

Answer 1

try and let us know (can't test your code ) :

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()