import Bio
from Bio import SeqIO
from Bio.SeqRecord import SeqRecord
from Bio.Seq import Seq
import argparse
import re
from numpy import array

parser = argparse.ArgumentParser()
parser.add_argument("-i", "--fasta_in", help="sequences to be scrambled")
parser.add_argument("-o", "--output_file", help="file to write ORFs to")
parser.add_argument("-r", "--replicate_number", help="number of scrambled sequences to generate", type=int, default=10)
parser.add_argument("-d", "--dont_demand_orf", help="simply shuffle the sequence, don't insist that it be a length-matched ORF", action="store_true", default=False)
parser.add_argument("-p", "--peptide_fasta", help="input fasta is an amino acid sequence - don't do nucleotide steps", action="store_true", default=False)


#parser.add_argument("-c", "--length_cutoff", help="ignore ORFs with fewer internal (ie, not start or stops) codons", type=int, default=75)
#parser.add_argument("-x", "--extend_across_gaps", help="extend the ORF even if it encounters a gap/N", action="store_true", default=False)
#parser.add_argument("-a", "--include_all_starts", help="report all ORFs when multiple start codons present (else choose longest)", action="store_true", default=False)

args = parser.parse_args()


#include_all_starts = args.include_all_starts
#length_cutoff = args.length_cutoff
#extend_across_gaps = args.extend_across_gaps
#reverse_complement = args.reverse_complement


