When running this code on a fasta file and a max() arg error occurs

Question

[rt2421]

from Bio import AlignIO
from Bio import SeqIO
from Bio import Seq
import os

input_file = "/Users/richard/Desktop/texas1.fasta"
records = SeqIO.parse(input_file, 'fasta')
records = list(records)

maxlen = max(len(record.seq) for record in records)

# pad sequences so that they all have the same length
for record in records:
    if len(record.seq) != maxlen:
        sequence = str(record.seq).ljust(maxlen, '.')
        record.seq = Seq.Seq(sequence)
assert all(len(record.seq) == maxlen for record in records)


output_file = '{}_padded.fasta'.format(os.path.splitext(input_file)[0])
with open(output_file, 'w') as f:
    SeqIO.write(records, f, 'fasta')
alignment = AlignIO.read(output_file, "fasta")
print (alignment)

The Error that occurs in line 10 and is ValueError: max() arg is an empty sequence. Could it be that the fasta file is too big?

[shenwei356]

Check records first by printing it.

[rt2421]

Thank you, it looks like the file is empty. It actually looks like there are amino acid sequences and not nucleotide sequences in the fasta file.