File: combine_contigs.py

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#!/usr/bin/python3
import sys
import os
import os.path
from Bio import SeqIO
from common import sample_name

files = sys.argv[1:]

output = sys.stdout

for file in files:
    for seq in SeqIO.parse(file, "fasta"):
        seq.id = sample_name(file) + "-" + seq.id
        seq.description = ""
        SeqIO.write(seq, output, "fasta")