BioPython SeqIO: [Errno 2] No such file or directory: 'd'

Question

I am trying to loop through a large fasta file with SeqIO.parse, but I am having some issues. Here is my test script as example:

from Bio import SeqIO

file = 'large.fasta'

for seq_record in SeqIO.parse(file[0], 'fasta'):
    print (seq_record)

The error it gives is:

Traceback (most recent call last):
  File "test.py", line 12, in <module>
    for seq_record in SeqIO.parse(file[0], 'fasta'):
  File "/Users/francoiskroll/miniconda3/lib/python3.6/site-packages/Bio/SeqIO/__init__.py", line 618, in parse
    with as_handle(handle, mode) as fp:
  File "/Users/francoiskroll/miniconda3/lib/python3.6/contextlib.py", line 81, in __enter__
    return next(self.gen)
  File "/Users/francoiskroll/miniconda3/lib/python3.6/site-packages/Bio/File.py", line 101, in as_handle
    with open(handleish, mode, **kwargs) as fp:
FileNotFoundError: [Errno 2] No such file or directory: 'l'

Can you help?

Answer 1

The first letter of your file is a d, because if file is a string, file[0] is the first character

for seq_record in SeqIO.parse(file, 'fasta'):
    print (seq_record)