DNA to peptide translation and adding to csv file

Question

[Sara]

I have a big csv file with DNA sequences like this small example (infile.csv):

2840,GTGGCCCGGGAGGCC
291,GCATGTCCGTAGGTTCGT
147,GCATGTCCG

I need to translate each DNA sequence to peptide sequence and add the 3rd column which will be the peptide sequence. here is the expected output:

2840,GTGGCCCGGGAGGCC,VAREA
291,GCATGTCCGTAGGTTCGT,ACP*VR
147,GCATGTCCG,ACP

to do so, I made small following code:

import pandas
df = pandas.read_csv('infile.csv')
seq = csv_data[1]

def translate(seq):
    table = {
        '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':'*', 'TAG':'*',
        'TGC':'C', 'TGT':'C', 'TGA':'*', 'TGG':'W',
    }
    protein =""
    if len(seq)%3 == 0:
        for i in range(0, len(seq), 3):
            codon = seq[i:i + 3]
            protein+= table[codon]
    return protein


peptide_seq=translate(seq)
df[peptide_seq]
df.to_csv("outfile.csv")

but it does not return the expected output. do you know how I can change the code to get the expected output?

Answer 1

[Mensur Dlakic]

There are several assignment errors above that I won't discuss in detail - you should be able to figure it out from the corrected code below.

import pandas
df = pandas.read_csv('infile.csv', header=None)
df.columns = ['index','DNA_sequence']
seq = df['DNA_sequence']

def translate(seq):
    table = {
        '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':'*', 'TAG':'*',
        'TGC':'C', 'TGT':'C', 'TGA':'*', 'TGG':'W',
    }
    protein = ''
    if len(seq)%3 == 0:
        for i in range(0, len(seq), 3):
            codon = seq[i:i + 3]
            protein += table[codon]
    return protein

peptide_seq = []
for j in range(len(seq)):
    peptide_seq.append(translate(seq[j]))
df['peptide_sequence'] = peptide_seq
df.to_csv('outfile.csv', index=False)

Answer 2

[Pierre Lindenbaum]

$ echo -e "2840,GTGGCCCGGGAGGCC\n291,GCATGTCCGTAGGTTCGT\n147,GCATGTCCG"  | awk -F, 'function translate(S) {L=length(S);P="";for(i=1;i+2<=L;i+=3) P=sprintf("%s%s",P,h[substr(S,i,3)]);return P;} BEGIN{h["AAA"]="K";h["AAC"]="N";h["AAG"]="K";h["AAT"]="N";h["ACA"]="T";h["ACC"]="T";h["ACG"]="T";h["ACT"]="T";h["AGA"]="R";h["AGC"]="S";h["AGG"]="R";h["AGT"]="S";h["ATA"]="I";h["ATC"]="I";h["ATG"]="M";h["ATT"]="I";h["CAA"]="Q";h["CAC"]="H";h["CAG"]="Q";h["CAT"]="H";h["CCA"]="P";h["CCC"]="P";h["CCG"]="P";h["CCT"]="P";h["CGA"]="R";h["CGC"]="R";h["CGG"]="R";h["CGT"]="R";h["CTA"]="L";h["CTC"]="L";h["CTG"]="L";h["CTT"]="L";h["GAA"]="E";h["GAC"]="D";h["GAG"]="E";h["GAT"]="D";h["GCA"]="A";h["GCC"]="A";h["GCG"]="A";h["GCT"]="A";h["GGA"]="G";h["GGC"]="G";h["GGG"]="G";h["GGT"]="G";h["GTA"]="V";h["GTC"]="V";h["GTG"]="V";h["GTT"]="V";h["TAA"]="*";h["TAC"]="Y";h["TAG"]="*";h["TAT"]="Y";h["TCA"]="S";h["TCC"]="S";h["TCG"]="S";h["TCT"]="S";h["TGA"]="*";h["TGC"]="C";h["TGG"]="W";h["TGT"]="C";h["TTA"]="L";h["TTC"]="F";h["TTG"]="L";h["TTT"]="F";} {OFS=",";print $1,$2,translate($2);}'

2840,GTGGCCCGGGAGGCC,VAREA
291,GCATGTCCGTAGGTTCGT,ACP*VR
147,GCATGTCCG,ACP