Error with frame/translation in BioPython?

Question

[alsxm9608220073]

I want to create a program that translates DNA sequences into amino acid sequences. So I used Biopython. here's what i have so far

import sys
from Bio import SeqIO
import warnings
warnings.filterwarnings("ignore")
filename = raw_input("Enter filename : ")
myfile = open(filename)
fasta_in=filename

for record in SeqIO.parse(fasta_in,'fasta'):
     id_part=record.id
     desc_part=record.description
     seq = record.seq

     print('seq:',seq)

print(seq);
frame_num = raw_input("Enter frame number: ")
if (frame_num[0] == '+'):
   for codon in [seq[i:i+3] for i in range(int(frame_num[1])-1, len(seq), 3)]:
      print seq.translate()
      sys.exit()



else:
for codon in [seq[i-3:i] for i in range(len(seq)-int(frame_num[1])+1, 0, -3)]:
    print seq.translate()
    sys.exit

I ran this program, but the same amino acid sequence translation was printed at +1 and -2. Like this:

Enter filename : ringo.txt
('seq:', Seq('TTCAGGAGTGGAACGCACGCCAGCGACGTCCAAGAAGCCTTGAAACAGTTCGTC...TTT', SingleLetterAlphabet()))
('seq:', Seq('ATGGGAAGAAGGCGAAGTCATGAGCGCCGGGATTTACCCCCTAACCTTTATATA...TAA', SingleLetterAlphabet()))ATGGGAAGAAGGCGAAGTCATGAGCGCCGGGATTTACCCCCTAACCTTTATATAAGAAACAATGGATATTACTGCTACAGGGACCCAAGGACGGGTAAAGAGTTTGGATTAGGCAGAGACAGGCGAATCGCAATCACTGAAGCTATACAGGCCAACATTGAGTTATTTTCAGGACACAAACACAAGCCTCTGACAGCGAGAATCAACAGTGATAATTCCGTTACGTTACATTCATGGCTTGATCGCTACGAAAAAATCCTGGCCAGCAGAGGAATCAAGCAGAAGACACTCATAAATTACATGAGCAAAATTAAAGCAATAAGGAGGGGTCTGCCTGATGCTCCACTTGAAGACATCACCACAAAAGAAATTGCGGCAATGCTCAATGGATACATAGACGAGGGCAAGGCGGCGTCAGCCAAGTTAATCAGATCAACACTGAGCGATGCATTCCGAGAGGCAATAGCTGAAGGCCATATAACAACAAACCATGTCGCTGCCACTCGCGCAGCAAAATCAGAGGTAAGGAGATCAAGACTTACGGCTGACGAATACCTGAAAATTTATCAAGCAGCAGAATCATCACCATGTTGGCTCAGACTTGCAATGGAACTGGCTGTTGTTACCGGGCAACGAGTTGGTGATTTATGCGAAATGAAGTGGTCTGATATCGTAGATGGATATCTTTATGTCGAGCAAAGCAAAACAGGCGTAAAAATTGCCATCCCAACAGCATTGCATATTGATGCTCTCGGAATATCAATGAAGGAAACACTTGATAAATGCAAAGAGATTCTTGGCGGAGAAACCATAATTGCATCTACTCGTCGCGAACCGCTTTCATCCGGCACAGTATCAAGGTATTTTATGCGCGCACGAAAAGCATCAGGTCTTTCCTTCGAAGGGGATCCGCCTACCTTTCACGAGTTGCGCAGTTTGTCTGCAAGACTCTATGAGAAGCAGATAAGCGATAAGTTTGCTCAACATCTTCTCGGGCATAAGTCGGACACCATGGCATCACAGTATCGTGATGACAGAGGCAGGGAGTGGGACAAAATTGAAATCAAATAA
Enter frame number: +1


MGRRRSHERRDLPPNLYIRNNGYYCYRDPRTGKEFGLGRDRRIAITEAIQANIELFSGHKHKPLTARINSDNSVTLHSWLDRYEKILASRGIKQKTLINYMSKIKAIRRGLPDAPLEDITTKEIAAMLNGYIDEGKAASAKLIRSTLSDAFREAIAEGHITTNHVAATRAAKSEVRRSRLTADEYLKIYQAAESSPCWLRLAMELAVVTGQRVGDLCEMKWSDIVDGYLYVEQSKTGVKIAIPTALHIDALGISMKETLDKCKEILGGETIIASTRREPLSSGTVSRYFMRARKASGLSFEGDPPTFHELRSLSARLYEKQISDKFAQHLLGHKSDTMASQYRDDRGREWDKIEIK*

And '-2'

Enter filename : ringo.txt
('seq:', Seq('TTCAGGAGTGGAACGCACGCCAGCGACGTCCAAGAAGCCTTGAAACAGTTCGTC...TTT', SingleLetterAlphabet()))
('seq:', Seq('ATGGGAAGAAGGCGAAGTCATGAGCGCCGGGATTTACCCCCTAACCTTTATATA...TAA', SingleLetterAlphabet()))ATGGGAAGAAGGCGAAGTCATGAGCGCCGGGATTTACCCCCTAACCTTTATATAAGAAACAATGGATATTACTGCTACAGGGACCCAAGGACGGGTAAAGAGTTTGGATTAGGCAGAGACAGGCGAATCGCAATCACTGAAGCTATACAGGCCAACATTGAGTTATTTTCAGGACACAAACACAAGCCTCTGACAGCGAGAATCAACAGTGATAATTCCGTTACGTTACATTCATGGCTTGATCGCTACGAAAAAATCCTGGCCAGCAGAGGAATCAAGCAGAAGACACTCATAAATTACATGAGCAAAATTAAAGCAATAAGGAGGGGTCTGCCTGATGCTCCACTTGAAGACATCACCACAAAAGAAATTGCGGCAATGCTCAATGGATACATAGACGAGGGCAAGGCGGCGTCAGCCAAGTTAATCAGATCAACACTGAGCGATGCATTCCGAGAGGCAATAGCTGAAGGCCATATAACAACAAACCATGTCGCTGCCACTCGCGCAGCAAAATCAGAGGTAAGGAGATCAAGACTTACGGCTGACGAATACCTGAAAATTTATCAAGCAGCAGAATCATCACCATGTTGGCTCAGACTTGCAATGGAACTGGCTGTTGTTACCGGGCAACGAGTTGGTGATTTATGCGAAATGAAGTGGTCTGATATCGTAGATGGATATCTTTATGTCGAGCAAAGCAAAACAGGCGTAAAAATTGCCATCCCAACAGCATTGCATATTGATGCTCTCGGAATATCAATGAAGGAAACACTTGATAAATGCAAAGAGATTCTTGGCGGAGAAACCATAATTGCATCTACTCGTCGCGAACCGCTTTCATCCGGCACAGTATCAAGGTATTTTATGCGCGCACGAAAAGCATCAGGTCTTTCCTTCGAAGGGGATCCGCCTACCTTTCACGAGTTGCGCAGTTTGTCTGCAAGACTCTATGAGAAGCAGATAAGCGATAAGTTTGCTCAACATCTTCTCGGGCATAAGTCGGACACCATGGCATCACAGTATCGTGATGACAGAGGCAGGGAGTGGGACAAAATTGAAATCAAATAA
Enter frame number: -2
MGRRRSHERRDLPPNLYIRNNGYYCYRDPRTGKEFGLGRDRRIAITEAIQANIELFSGHKHKPLTARINSDNSVTLHSWLDRYEKILASRGIKQKTLINYMSKIKAIRRGLPDAPLEDITTKEIAAMLNGYIDEGKAASAKLIRSTLSDAFREAIAEGHITTNHVAATRAAKSEVRRSRLTADEYLKIYQAAESSPCWLRLAMELAVVTGQRVGDLCEMKWSDIVDGYLYVEQSKTGVKIAIPTALHIDALGISMKETLDKCKEILGGETIIASTRREPLSSGTVSRYFMRARKASGLSFEGDPPTFHELRSLSARLYEKQISDKFAQHLLGHKSDTMASQYRDDRGREWDKIEIK*

I want to make program like this

Ask the user for a file name in FASTA format. Open the file (while checking for errors. Input the frame number (+1, +2, +3, -1, -2, -3) from the user. Output the amino acid sequence when read from the input frame.

I don't know what to fix. If you know a good solution, please let me know.

[Ram]

Hi, is this a homework/assignment question?

[Joe]

Just FYI, OP, I’ve edited your tags (the # are not necessary) to make it easier for people watching the tags to find your post, and I’ve altered your title to be a bit more specific to the question. If you would like to rephrase my change, please feel free, but try to keep the title descriptive of the thread content.

[Joe]

BioPython is smart enough that you don’t need to get your hands quite so dirty with the codons and frames.

There is a whole module of sequence utilities which includes a 6 frame translator, so you can translate everything at once:

https://biopython.org/DIST/docs/api/Bio.SeqUtils-module.html#six_frame_translations

[Eric Lim]

While I like that util, I think its main purpose is to prettify things. I find it difficult to work with the string representation of the translations.

[Joe]

True, though OP could probably extract the relevant bits of the source for their problem. Looping over each triplet individually to translate them doesn’t strike me as efficient/robust/necessary