mRNA/DNA to protein - fasta

Question

The code that I am trying to produce is about translating a FASTA-file that contains nucleotides (U, T, C, G or A) from DNA or mRNA into amino acids. It went very well, but when I run my program, it reports some mistakes that I don't understand, even though I tried to fix it, it just doesn't work. Could you guys give me some tips? I searched some possible solutions, but it was too difficult for me to understand.
My code
#!/bin/usr/env python3
import sys
codontable = {
'ATA':'I', 'ATC':'I', 'ATT':'I', 'ATG':'M',
'ACA':'T', 'ACC':'T', 'ACG':'T', 'ACT':'T',
'AAC':'N', 'AAT':'N', 'AAA':'K', 'AAG':'K',
'AGC':'S', 'AGT':'S', 'AGA':'R', 'AGG':'R',
'CTA':'L', 'CTC':'L', 'CTG':'L', 'CTT':'L',
'CCA':'P', 'CCC':'P', 'CCG':'P', 'CCT':'P',
'CAC':'H', 'CAT':'H', 'CAA':'Q', 'CAG':'Q',
'CGA':'R', 'CGC':'R', 'CGG':'R', 'CGT':'R',
'GTA':'V', 'GTC':'V', 'GTG':'V', 'GTT':'V',
'GCA':'A', 'GCC':'A', 'GCG':'A', 'GCT':'A',
'GAC':'D', 'GAT':'D', 'GAA':'E', 'GAG':'E',
'GGA':'G', 'GGC':'G', 'GGG':'G', 'GGT':'G',
'TCA':'S', 'TCC':'S', 'TCG':'S', 'TCT':'S',
'TTC':'F', 'TTT':'F', 'TTA':'L', 'TTG':'L',
'TAC':'Y', 'TAT':'Y', 'TAA':'Stop', 'TAG':'Stop',
'TGC':'C', 'TGT':'C', 'TGA':'Stop', 'TGG':'W',
'AUA':'I', 'AUC':'I', 'AUU':'I', 'AUG':'M',
'ACU':'U', 'AAU':'N', 'AGU':'S', 'CUA':'L',
'CUG':'L', 'CUG':'L', 'CUU':'L', 'CCU':'P',
'CAU':'H', 'CGU':'R', 'GUA':'V', 'GUC':'V',
'GUG':'V', 'GUU':'V', 'GCU':'A', 'GAU':'D',
'GGU':'G', 'UCA':'S', 'UCC':'S', 'UCG':'S',
'UCU':'S', 'UUC':'F', 'UUU':'F', 'UUA':'L',
'UUG':'L', 'UAC':'Y', 'UAU':'Y', 'UAA':'Stop',
'UAG':'Stop', 'UGC':'C', 'UGU':'C', 'UGA':'Stop',
'UGG':'W'}
def divideintriplets(startwhere, moveover = 3):
startwhere = int(startwhere)
moveover = int(moveover)
readwhere = startwhere + moveover
triplet = sequence[startwhere:readwhere]
amino = codontable[triplet]
lentriplet = len(triplet)
if lentriplet == 3:
return amino
else:
return None
list_trans_nucl = []
filenames = sys.argv[1:]
startwhere = input('n\Where to start with counting? Choose one; \n1: Start counting at the first nucleotide. \n2: Start counting at the second nucleotide. \n3: Start counting at the third nucleotide. \n')
for file in filenames:
count = 0
contains_aminoacid = False
inputfile = open(file)
for line in inputfile:
if not line.startswith('>'):
sequence = line.strip("")
count += len(sequence)
trans_nucl = divideintriplets(startwhere)
list_trans_nucl.append(trans_nucl)
for element in sequence:
if element not in ['A', 'T', 'C', 'G', 'U']:
contains_aminoacid = True
if contains_aminoacid is False:
print(list_trans_nucl)
print("This file contains ", count, "nucleotides")
What my command prompt says what is wrong
Traceback (most recent call last):
File "C:\Users\Desktop\CCR5\DNA_mRNA_translator.py", line 61, in <module>
trans_nucl = divideintriplets(startwhere)
File "C:\Users\Desktop\CCR5\DNA_mRNA_translator.py", line 41, in divideintriplets
amino = codontable[triplet]
KeyError: ''
>gi|255652911:5001-11065 | Homo sapiens chemokine (C-C motif) receptor 5 (gene/pseudogene) (CCR5), RefSeqGene on chromosome 3
CTTCAGATAGATTATATCTGGAGTGAAGAATCCTGCCACCTATGTATCTGGCATAGTGTGAGTCCTCATA
AATGCTTACTGGTTTGAAGGGCAACAAAATAGTGAACAGAGTGAAAATCCCCACTAAGATCCTGGGTCCA
GAAAAAGATGGGAAACCTGTTTAGCTCACCCGTGAGCCCATAGTTAAAACTCTTTAGACAACAGGTTGTT
TCCGTTTACAGAGAACAATAATATTGGGTGGTGAGCATCTGTGTGGGGGTTGGGGTGGGATAGGGGATAC
GGGGAGAGTGGAGAAAAAGGGGACACAGGGTTAATGTGAAGTCCAGGATCCCCCTCTACATTTAAAGTTG
GTTTAAGTTGGCTTTAATTAATAGCAACTCTTAAGATAATCAGAATTTTCTTAACCTTTTAGCCTTACTG
TTGAAAAGCCCTGTGATCTTGTACAAATCATTTGCTTCTTGGATAGTAATTTCTTTTACTAAAATGTGGG
CTTTTGACTAGATGAATGTAAATGTTCTTCTAGCTCTGATATCCTTTATTCTTTATATTTTCTAACAGAT
TCTGTGTAGTGGGATGAGCAGAGAACAAAAACAAAATAATCCAGTGAGAAAAGCCCGTAAATAAACCTTC
AGACCAGAGATCTATTCTCTAGCTTATTTTAAGCTCAACTTAAAAAGAAGAACTGTTCTCTGATTCTTTT
CGCCTTCAATACACTTAATGATTTAACTCCACCCTCCTTCAAAAGAAACAGCATTTCCTACTTTTATACT
GTCTATATGATTGATTTGCACAGCTCATCTGGCCAGAAGAGCTGAGACATCCGTTCCCCTACAAGAAACT
CTCCCCGGTAAGTAACCTCTCAGCTGCTTGGCCTGTTAGTTAGCTTCTGAGATGAGTAAAAGACTTTACA
GGAAACCCATAGAAGACATTTGGCAAACACCAAGTGCTCATACAATTATCTTAAAATATAATCTTTAAGA
TAAGGAAAGGGTCACAGTTTGGAATGAGTTTCAGACGGTTATAACATCAAAGATACAAAACATGATTGTG
AGTGAAAGACTTTAAAGGGAGCAATAGTATTTTAATAACTAACAATCCTTACCTCTCAAAAGAAAGATTT
GCAGAGAGATGAGTCTTAGCTGAAATCTTGAAATCTTATCTTCTGCTAAGGAGAACTAAACCCTCTCCAG
TGAGATGCCTTCTGAATATGTGCCCACAAGAAGTTGTGTCTAAGTCTGGTTCTCTTTTTTCTTTTTCCTC
CAGACAAGAGGGAAGCCTAAAAATGGTCAAAATTAATATTAAATTACAAACGCCAAATAAAATTTTCCTC
TAATATATCAGTTTCATGGCACAGTTAGTATATAATTCTTTATGGTTCAAAATTAAAAATGAGCTTTTCT
AGGGGCTTCTCTCAGCTGCCTAGTCTAAGGTGCAGGGAGTTTGAGACTCACAGGGTTTAATAAGAGAAAA
TTCTCAGCTAGAGCAGCTGAACTTAAATAGACTAGGCAAGACAGCTGGTTATAAGACTAAACTACCCAGA
ATGCATGACATTCATCTGTGGTGGCAGACGAAACATTTTTTATTATATTATTTCTTGGGTATGTATGACA
ACTCTTAATTGTGGCAACTCAGAAACTACAAACACAAACTTCACAGAAAATGTGAGGATTTTACAATTGG
CTGTTGTCATCTATGACCTTCCCTGGGACTTGGGCACCCGGCCATTTCACTCTGACTACATCATGTCACC
AAACATCTGATGGTCTTGCCTTTTAATTCTCTTTTCGAGGACTGAGAGGGAGGGTAGCATGGTAGTTAAG
AGTGCAGGCTTCCCGCATTCAAAATCGGTTGCTTACTAGCTGTGTGGCTTTGAGCAAGTTACTCACCCTC
TCTGTGCTTCAAGGTCCTTGTCTGCAAAATGTGAAAAATATTTCCTGCCTCATAAGGTTGCCCTAAGGAT
TAAATGAATGAATGGGTATGATGCTTAGAACAGTGATTGGCATCCAGTATGTGCCCTCGAGGCCTCTTAA
TTATTACTGGCTTGCTCATAGTGCATGTTCTTTGTGGGCTAACTCTAGCGTCAATAAAAATGTTAAGACT
GAGTTGCAGCCGGGCATGGTGGCTCATGCCTGTAATCCCAGCATTCTAGGAGGCTGAGGCAGGAGGATCG
CTTGAGCCCAGGAGTTCGAGACCAGCCTGGGCAACATAGTGTGATCTTGTATCTATAAAAATAAACAAAA
TTAGCTTGGTGTGGTGGCGCCTGTAGTCCCCAGCCACTTGGAGGGGTGAGGTGAGAGGATTGCTTGAGCC
CGGGATGGTCCAGGCTGCAGTGAGCCATGATCGTGCCACTGCACTCCAGCCTGGGCGACAGAGTGAGACC
CTGTCTCACAACAACAACAACAACAACAAAAAGGCTGAGCTGCACCATGCTTGACCCAGTTTCTTAAAAT
TGTTGTCAAAGCTTCATTCACTCCATGGTGCTATAGAGCACAAGATTTTATTTGGTGAGATGGTGCTTTC
ATGAATTCCCCCAACAGAGCCAAGCTCTCCATCTAGTGGACAGGGAAGCTAGCAGCAAACCTTCCCTTCA
CTACAAAACTTCATTGCTTGGCCAAAAAGAGAGTTAATTCAATGTAGACATCTATGTAGGCAATTAAAAA
CCTATTGATGTATAAAACAGTTTGCATTCATGGAGGGCAACTAAATACATTCTAGGACTTTATAAAAGAT
CACTTTTTATTTATGCACAGGGTGGAACAAGATGGATTATCAAGTGTCAAGTCCAATCTATGACATCAAT
TATTATACATCGGAGCCCTGCCAAAAAATCAATGTGAAGCAAATCGCAGCCCGCCTCCTGCCTCCGCTCT
ACTCACTGGTGTTCATCTTTGGTTTTGTGGGCAACATGCTGGTCATCCTCATCCTGATAAACTGCAAAAG
GCTGAAGAGCATGACTGACATCTACCTGCTCAACCTGGCCATCTCTGACCTGTTTTTCCTTCTTACTGTC
CCCTTCTGGGCTCACTATGCTGCCGCCCAGTGGGACTTTGGAAATACAATGTGTCAACTCTTGACAGGGC
TCTATTTTATAGGCTTCTTCTCTGGAATCTTCTTCATCATCCTCCTGACAATCGATAGGTACCTGGCTGT
CGTCCATGCTGTGTTTGCTTTAAAAGCCAGGACGGTCACCTTTGGGGTGGTGACAAGTGTGATCACTTGG
GTGGTGGCTGTGTTTGCGTCTCTCCCAGGAATCATCTTTACCAGATCTCAAAAAGAAGGTCTTCATTACA
CCTGCAGCTCTCATTTTCCATACAGTCAGTATCAATTCTGGAAGAATTTCCAGACATTAAAGATAGTCAT
CTTGGGGCTGGTCCTGCCGCTGCTTGTCATGGTCATCTGCTACTCGGGAATCCTAAAAACTCTGCTTCGG
TGTCGAAATGAGAAGAAGAGGCACAGGGCTGTGAGGCTTATCTTCACCATCATGATTGTTTATTTTCTCT
TCTGGGCTCCCTACAACATTGTCCTTCTCCTGAACACCTTCCAGGAATTCTTTGGCCTGAATAATTGCAG
TAGCTCTAACAGGTTGGACCAAGCTATGCAGGTGACAGAGACTCTTGGGATGACGCACTGCTGCATCAAC
CCCATCATCTATGCCTTTGTCGGGGAGAAGTTCAGAAACTACCTCTTAGTCTTCTTCCAAAAGCACATTG
CCAAACGCTTCTGCAAATGCTGTTCTATTTTCCAGCAAGAGGCTCCCGAGCGAGCAAGCTCAGTTTACAC
CCGATCCACTGGGGAGCAGGAAATATCTGTGGGCTTGTGACACGGACTCAAGTGGGCTGGTGACCCAGTC
AGAGTTGTGCACATGGCTTAGTTTTCATACACAGCCTGGGCTGGGGGTGGGGTGGGAGAGGTCTTTTTTA
AAAGGAAGTTACTGTTATAGAGGGTCTAAGATTCATCCATTTATTTGGCATCTGTTTAAAGTAGATTAGA
TCTTTTAAGCCCATCAATTATAGAAAGCCAAATCAAAATATGTTGATGAAAAATAGCAACCTTTTTATCT
CCCCTTCACATGCATCAAGTTATTGACAAACTCTCCCTTCACTCCGAAAGTTCCTTATGTATATTTAAAA
GAAAGCCTCAGAGAATTGCTGATTCTTGAGTTTAGTGATCTGAACAGAAATACCAAAATTATTTCAGAAA
TGTACAACTTTTTACCTAGTACAAGGCAACATATAGGTTGTAAATGTGTTTAAAACAGGTCTTTGTCTTG
CTATGGGGAGAAAAGACATGAATATGATTAGTAAAGAAATGACACTTTTCATGTGTGATTTCCCCTCCAA
GGTATGGTTAATAAGTTTCACTGACTTAGAACCAGGCGAGAGACTTGTGGCCTGGGAGAGCTGGGGAAGC
TTCTTAAATGAGAAGGAATTTGAGTTGGATCATCTATTGCTGGCAAAGACAGAAGCCTCACTGCAAGCAC
TGCATGGGCAAGCTTGGCTGTAGAAGGAGACAGAGCTGGTTGGGAAGACATGGGGAGGAAGGACAAGGCT
AGATCATGAAGAACCTTGACGGCATTGCTCCGTCTAAGTCATGAGCTGAGCAGGGAGATCCTGGTTGGTG
TTGCAGAAGGTTTACTCTGTGGCCAAAGGAGGGTCAGGAAGGATGAGCATTTAGGGCAAGGAGACCACCA
ACAGCCCTCAGGTCAGGGTGAGGATGGCCTCTGCTAAGCTCAAGGCGTGAGGATGGGAAGGAGGGAGGTA
TTCGTAAGGATGGGAAGGAGGGAGGTATTCGTGCAGCATATGAGGATGCAGAGTCAGCAGAACTGGGGTG
GATTTGGGTTGGAAGTGAGGGTCAGAGAGGAGTCAGAGAGAATCCCTAGTCTTCAAGCAGATTGGAGAAA
CCCTTGAAAAGACATCAAGCACAGAAGGAGGAGGAGGAGGTTTAGGTCAAGAAGAAGATGGATTGGTGTA
AAAGGATGGGTCTGGTTTGCAGAGCTTGAACACAGTCTCACCCAGACTCCAGGCTGTCTTTCACTGAATG
CTTCTGACTTCATAGATTTCCTTCCCATCCCAGCTGAAATACTGAGGGGTCTCCAGGAGGAGACTAGATT
TATGAATACACGAGGTATGAGGTCTAGGAACATACTTCAGCTCACACATGAGATCTAGGTGAGGATTGAT
TACCTAGTAGTCATTTCATGGGTTGTTGGGAGGATTCTATGAGGCAACCACAGGCAGCATTTAGCACATA
CTACACATTCAATAAGCATCAAACTCTTAGTTACTCATTCAGGGATAGCACTGAGCAAAGCATTGAGCAA
AGGGGTCCCATAGAGGTGAGGGAAGCCTGAAAAACTAAGATGCTGCCTGCCCAGTGCACACAAGTGTAGG
TATCATTTTCTGCATTTAACCGTCAATAGGCAAAGGGGGGAAGGGACATATTCATTTGGAAATAAGCTGC
CTTGAGCCTTAAAACCCACAAAAGTACAATTTACCAGCCTCCGTATTTCAGACTGAATGGGGGTGGGGGG
GGCGCCTTAGGTACTTATTCCAGATGCCTTCTCCAGACAAACCAGAAGCAACAGAAAAAATCGTCTCTCC
CTCCCTTTGAAATGAATATACCCCTTAGTGTTTGGGTATATTCATTTCAAAGGGAGAGAGAGAGGTTTTT
TTCTGTTCTGTCTCATATGATTGTGCACATACTTGAGACTGTTTTGAATTTGGGGGATGGCTAAAACCAT
CATAGTACAGGTAAGGTGAGGGAATAGTAAGTGGTGAGAACTACTCAGGGAATGAAGGTGTCAGAATAAT
AAGAGGTGCTACTGACTTTCTCAGCCTCTGAATATGAACGGTGAGCATTGTGGCTGTCAGCAGGAAGCAA
CGAAGGGAAATGTCTTTCCTTTTGCTCTTAAGTTGTGGAGAGTGCAACAGTAGCATAGGACCCTACCCTC
TGGGCCAAGTCAAAGACATTCTGACATCTTAGTATTTGCATATTCTTATGTATGTGAAAGTTACAAATTG
CTTGAAAGAAAATATGCATCTAATAAAAAACACCTTCTAAAATAA

Answer 1

This code has a number of problems:
1) This is a no-op?
sequence = line.strip("")
I suggest:
sequence = line.rstrip()
until you've had a chance to read up on strip() and its variants.
2) This test comes after the code that assumes the data is OK:
amino = codontable[triplet]
lentriplet = len(triplet)
if lentriplet == 3:
If lentriplet wasn't 3, should you have looked it up in codontable?
3) This test comes after the code that assumes the data is OK:
trans_nucl = divideintriplets(startwhere)
...
for element in sequence:
if element not in ['A', 'T', 'C', 'G', 'U']:
contains_aminoacid = True
if contains_aminoacid is False:
If this wasn't a nuecleotide sequence, why did you first divide it into triplets? Test first, proceed if OK. Not the other way 'round.
4) necleotide sequence 'CUG' is defined twice in the dictionary.
5) divideintriplets shouldn't return None on error if the caller isn't checking for any error:
trans_nucl = divideintriplets(startwhere)
list_trans_nucl.append(trans_nucl)
6) That critical "you seem to be just pulling off the first triplet, and throwing the rest away" thing that #JohnColeman mentioned.
7) Other stuff like list_trans_nucl = [] should be (re)initialized for each file, not just once.
My rework of your code, sans codon table:
import sys
codontable = {
...
}
def divideintriplets(sequence, startwhere, moveover=3):
codons = []
length = len(sequence)
readwhere = startwhere + moveover
while readwhere < length:
triplet = sequence[startwhere:readwhere]
assert len(triplet) == 3
assert triplet in codontable
codons.append(codontable[triplet])
startwhere += moveover
readwhere = startwhere + moveover
return codons
filenames = sys.argv[1:]
startwhere = input('\nWhere to start with counting? Choose one; \n1: Start counting at the first nucleotide. \n2: Start counting at the second nucleotide. \n3: Start counting at the third nucleotide. \n')
for filename in filenames:
list_trans_nucl = []
count = 0
contains_nuecleotides = True
with open(filename) as inputfile:
for line in inputfile:
if not line.startswith('>'):
sequence = line.rstrip()
for element in sequence:
if element not in 'ATCGU':
contains_nuecleotides = False
break
if not contains_nuecleotides:
break
count += len(sequence)
trans_nucl = divideintriplets(sequence, int(startwhere))
list_trans_nucl.extend(trans_nucl)
print(list_trans_nucl)
print("File", filename, "contains", count, "nucleotides")
OUTPUT
% python3 test.py file0.fasta
Where to start with counting? Choose one;
1: Start counting at the first nucleotide.
2: Start counting at the second nucleotide.
3: Start counting at the third nucleotide.
1
['F', 'R', 'Stop', 'I', 'I', 'S', 'G', 'V', 'K', 'N', 'P', 'A', 'T', 'Y', 'V', 'S', 'G', 'I', 'V', 'Stop', 'V', 'L', 'M', 'L', 'T', 'G', 'L', 'K', 'G', 'N', 'K', 'I', 'V', 'N', 'R', 'V', 'K', 'I', 'P', 'T', 'K', 'I', 'L', 'G', 'K', 'K', 'M', 'G', 'N', 'L', 'F', 'S', 'S', 'P', 'V', 'S', 'P', 'Stop', 'L', 'K', 'L', 'F', 'R', 'Q', 'Q', 'V', 'P', 'F', 'T', 'E', 'N', 'N', 'N', 'I', 'G', 'W', 'Stop', 'A', 'S', 'V', 'W', 'G', 'L', 'G', 'W', 'D', 'R', 'G', 'G', 'R', 'V', 'E', 'K', 'K', 'G', 'T', 'Q', 'G', 'Stop', 'C', 'E', 'V', 'Q', 'D', 'P', 'P', 'L', 'H', 'L', 'K', 'F', 'K', 'L', 'A', 'L', 'I', 'N', 'S', 'N', 'S', 'Stop', 'D', 'N', 'Q', 'N', 'F', 'L', 'N', 'L', 'L', 'A', 'L', 'Stop', 'K', 'A', 'L', 'Stop', 'S', 'C', 'T', 'N', 'H', 'L', 'L', 'L', 'G', 'Stop', 'Stop', 'F', 'L', 'L', 'L', 'K', 'C', 'F', 'Stop', 'L', 'D', 'E', 'C', 'K', 'C', 'S', 'S', 'S', 'S', 'D', 'I', 'L', 'Y', 'S', 'L', 'Y', 'F', 'L', 'T', 'L', 'C', 'S', 'G', 'M', 'S', 'R', 'E', 'Q', 'K', 'Q', 'N', 'N', 'P', 'V', 'R', 'K', 'A', 'R', 'K', 'Stop', 'T', 'D', 'Q', 'R', 'S', 'I', 'L', 'Stop', 'L', 'I', 'L', 'S', 'S', 'T', 'Stop', 'K', 'E', 'E', 'L', 'F', 'S', 'D', 'S', 'A', 'F', 'N', 'T', 'L', 'N', 'D', 'L', 'T', 'P', 'P', 'S', 'F', 'K', 'R', 'N', 'S', 'I', 'S', 'Y', 'F', 'Y', 'S', 'I', 'Stop', 'L', 'I', 'C', 'T', 'A', 'H', 'L', 'A', 'R', 'R', 'A', 'E', 'T', 'S', 'V', 'P', 'L', 'Q', 'E', 'S', 'P', 'V', 'S', 'N', 'L', 'S', 'A', 'A', 'W', 'P', 'V', 'S', 'Stop', 'L', 'L', 'R', 'Stop', 'V', 'K', 'D', 'F', 'E', 'T', 'H', 'R', 'R', 'H', 'L', 'A', 'N', 'T', 'K', 'C', 'S', 'Y', 'N', 'Y', 'L', 'K', 'I', 'Stop', 'S', 'L', 'K', 'E', 'R', 'V', 'T', 'V', 'W', 'N', 'E', 'F', 'Q', 'T', 'V', 'I', 'T', 'S', 'K', 'I', 'Q', 'N', 'M', 'I', 'V', 'K', 'D', 'F', 'K', 'G', 'S', 'N', 'S', 'I', 'L', 'I', 'T', 'N', 'N', 'P', 'Y', 'L', 'S', 'K', 'E', 'R', 'Q', 'R', 'D', 'E', 'S', 'Stop', 'L', 'K', 'S', 'Stop', 'N', 'L', 'I', 'F', 'C', 'Stop', 'G', 'E', 'L', 'N', 'P', 'L', 'E', 'M', 'P', 'S', 'E', 'Y', 'V', 'P', 'T', 'R', 'S', 'C', 'V', 'Stop', 'V', 'W', 'F', 'S', 'F', 'F', 'F', 'F', 'R', 'Q', 'E', 'G', 'S', 'L', 'K', 'M', 'V', 'K', 'I', 'N', 'I', 'K', 'L', 'Q', 'T', 'P', 'N', 'K', 'I', 'F', 'N', 'I', 'S', 'V', 'S', 'W', 'H', 'S', 'Stop', 'Y', 'I', 'I', 'L', 'Y', 'G', 'S', 'K', 'L', 'K', 'M', 'S', 'F', 'G', 'A', 'S', 'L', 'S', 'C', 'L', 'V', 'Stop', 'G', 'A', 'G', 'S', 'L', 'R', 'L', 'T', 'G', 'F', 'N', 'K', 'R', 'S', 'Q', 'L', 'E', 'Q', 'L', 'N', 'L', 'N', 'R', 'L', 'G', 'K', 'T', 'A', 'G', 'Y', 'K', 'T', 'K', 'L', 'P', 'C', 'M', 'T', 'F', 'I', 'C', 'G', 'G', 'R', 'R', 'N', 'I', 'F', 'Y', 'Y', 'I', 'I', 'S', 'W', 'V', 'C', 'M', 'L', 'L', 'I', 'V', 'A', 'T', 'Q', 'K', 'L', 'Q', 'T', 'Q', 'T', 'S', 'Q', 'K', 'M', 'Stop', 'G', 'F', 'Y', 'N', 'C', 'C', 'H', 'L', 'Stop', 'P', 'S', 'L', 'G', 'L', 'G', 'H', 'P', 'A', 'I', 'S', 'L', 'Stop', 'L', 'H', 'H', 'V', 'N', 'I', 'Stop', 'W', 'S', 'C', 'L', 'L', 'I', 'L', 'F', 'S', 'R', 'T', 'E', 'R', 'E', 'G', 'S', 'M', 'V', 'V', 'V', 'Q', 'A', 'S', 'R', 'I', 'Q', 'N', 'R', 'L', 'L', 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File file0.fasta contains 6065 nucleotides
%

Answer 2

From what I can see the problem is that the key '' does not exist in your initial variable codontable. My guess is that the input file you are providing has empty key/s.