Write a program in python using this template:

#!/usr/bin/env python """TODO: Say what the code does TODO: Elaborate on what the code does """ import argparse #TODO import other libraries needed def get_args(): """Return parsed command-line arguments.""" parser = argparse.ArgumentParser( description="TODO: say what the script does.", formatter_class=argparse.ArgumentDefaultsHelpFormatter) # get the FASTA file of sequences parser.add_argument('filename', # variable to access this data later: args.filename metavar='FASTA', # shorthand to represent the input value help='Provide name and path to FASTA file to process.', # message to the user, it goes into the help menu type=str) parser.add_argument('-p', '--pattern', # access with args.pattern help='Provide a regex pattern for filtering FASTA entries', default='^\d{1}\D*$') # default works for Drosophila chromosomes return(parser.parse_args()) def find_first_orf(rna): """Return first open-reading frame of RNA sequence as a Bio.Seq object. Must start with AUG Must end with UAA, UAG, or UGA Must have even multiple of 3 RNA bases between """ try: #TODO update regex to find the ORF orf = re.search('TODO: your regex', str(rna)).group() except AttributeError: # if no match found, orf should be empty orf = "" return(Seq(orf)) def translate_first_orf(dna): """TODO: what it does Assumes input sequences is a Bio.Seq object. """ # TODO: transcribe the DNA, find the first ORF, translate said ORF return(translated_orf) if __name__ == "__main__": #TODO: get command-line arguments #TODO: use SeqIO to get the records in the fasta file provided by the command-line input #TODO: if the FASTA record's ID matches the regex pattern, # then print out its record ID then a tab space then the translated first ORF That passes all these tests: 

#!user/bin/env python3 """Test behavior of translate_first_orf.py""" from translate_first_orf import find_first_orf from translate_first_orf import translate_first_orf from Bio.Seq import Seq def test_short_orf(): """Identify short ORF""" assert find_first_orf("AUGCCCUAG") == "AUGCCCUAG", "expect three codon ORF" def test_orf_in_orf(): """Identify first ORF when two present""" assert find_first_orf("AUGCUGUAACUGUAG") == "AUGCUGUAA", "expect first complete ORF" def test_missing_stop_codon(): """Identify no ORF when missing stop codon""" assert find_first_orf("AUGCUG") == "", "expect no ORF in AUGCUG - lacks stop codon" def test_out_of_frame_stop(): """Identify no ORF when stop codon is out of frame""" assert find_first_orf("AUGAUAA") == "", "expect no ORF in AUGAUAA - stop codon out of frame" def test_dna_sequence(): """Identify protein sequence within DNA""" assert translate_first_orf(Seq("AAATGCCCTAG")) == "MP*", "expect MP protein within sequence"