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import sys | ||
from Bio import SeqIO | ||
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# Get input and output file paths from command-line arguments | ||
# Daniel Paiva Agustinho | ||
input_file = sys.argv[1] | ||
output_file = sys.argv[2] | ||
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with open(input_file, "r") as input_handle: | ||
with open(output_file, "w") as output_handle: | ||
for record in SeqIO.parse(input_handle, "fasta"): | ||
protein_seq = record.seq.translate() | ||
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# Extract the entire original header | ||
original_header = record.description | ||
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# Create a new sequence record with the original header | ||
protein_seq = SeqIO.SeqRecord( | ||
protein_seq, id=record.id, description=original_header | ||
) | ||
SeqIO.write(protein_seq, output_handle, "fasta") | ||
print("done",str(output_file)) |