How do I convert the three letter amino acid codes to one letter code with python or R?

Question

I have a fasta file as shown below. I would like to convert the three letter codes to one letter code. How can I do this with python or R?

>2ppo
ARGHISLEULEULYS
>3oot
METHISARGARGMET

desired output

>2ppo
RHLLK
>3oot
MHRRM

your suggestions would be appreciated!!

Answer 1

BioPython already has built-in dictionaries to help with such translations. Following commands will show you a whole list of available dictionaries:

import Bio
help(Bio.SeqUtils.IUPACData)

The predefined dictionary you are looking for:

Bio.SeqUtils.IUPACData.protein_letters_3to1['Ala']

Answer 2

Use a dictionary to look up the one letter codes:

d = {'CYS': 'C', 'ASP': 'D', 'SER': 'S', 'GLN': 'Q', 'LYS': 'K',
     'ILE': 'I', 'PRO': 'P', 'THR': 'T', 'PHE': 'F', 'ASN': 'N', 
     'GLY': 'G', 'HIS': 'H', 'LEU': 'L', 'ARG': 'R', 'TRP': 'W', 
     'ALA': 'A', 'VAL':'V', 'GLU': 'E', 'TYR': 'Y', 'MET': 'M'}

And a simple function to match the three letter codes with one letter codes for the entire string:

def shorten(x):
    if len(x) % 3 != 0: 
        raise ValueError('Input length should be a multiple of three')

    y = ''
    for i in range(len(x)/3):
            y += d[x[3*i:3*i+3]]
    return y

Testing your example:

>>> shorten('ARGHISLEULEULYS')
'RHLLK'

Answer 3

Here is a way to do it in R:

# Variables:
foo <- c("ARGHISLEULEULYS","METHISARGARGMET")

# Code maps:
code3 <- c("Ala", "Arg", "Asn", "Asp", "Cys", "Glu", "Gln", "Gly", "His", 
"Ile", "Leu", "Lys", "Met", "Phe", "Pro", "Ser", "Thr", "Trp", 
"Tyr", "Val")
code1 <- c("A", "R", "N", "D", "C", "E", "Q", "G", "H", "I", "L", "K", 
"M", "F", "P", "S", "T", "W", "Y", "V")

# For each code replace 3letter code by 1letter code:
for (i in 1:length(code3))
{
    foo <- gsub(code3[i],code1[i],foo,ignore.case=TRUE)
}

Results in :

> foo
[1] "RHLLK" "MHRRM"

Note that I changed the variable name as variable names are not allowed to start with a number in R.

Answer 4

>>> src = "ARGHISLEULEULYS"
>>> trans = {'ARG':'R', 'HIS':'H', 'LEU':'L', 'LYS':'K'}
>>> "".join(trans[src[x:x+3]] for x in range(0, len(src), 3))
'RHLLK'

You just need to add the rest of the entries to the trans dict.

Edit:

To make the rest of trans , you can do this. File table :

Ala A
Arg R
Asn N
Asp D
Cys C
Glu E
Gln Q
Gly G
His H
Ile I
Leu L
Lys K
Met M
Phe F
Pro P
Ser S
Thr T
Trp W
Tyr Y
Val V

Read it:

trans = dict((l.upper(), s) for l, s in
             [row.strip().split() for row in open("table").readlines()])

Answer 5

You may try looking into and installing Biopython since you are parsing a .fasta file and then converting to one letter codes. Unfortunately, Biopython only has the function seq3(in package Bio::SeqUtils) which does the inverse of what you want. Example output in IDLE:

>>>seq3("MAIVMGRWKGAR*")
>>>'MetAlaIleValMetGlyArgTrpLysGlyAlaArgTer'

Unfortunately, there is no 'seq1' function (yet...) but I thought this might be helpful to you in the future. As far as your problem, Junuxx is correct. Create a dictionary and use a for loop to read the string in blocks of three and translate. Here is a similar function to the one he provided that is all-inclusive and handles lower cases as well.

def AAcode_3_to_1(seq):
    '''Turn a three letter protein into a one letter protein.

    The 3 letter code can be upper, lower, or any mix of cases
    The seq input length should be a factor of 3 or else results
    in an error

    >>>AAcode_3_to_1('METHISARGARGMET')
    >>>'MHRRM'

    '''
    d = {'CYS': 'C', 'ASP': 'D', 'SER': 'S', 'GLN': 'Q', 'LYS': 'K',
     'ILE': 'I', 'PRO': 'P', 'THR': 'T', 'PHE': 'F', 'ASN': 'N', 
     'GLY': 'G', 'HIS': 'H', 'LEU': 'L', 'ARG': 'R', 'TRP': 'W', 'TER':'*',
     'ALA': 'A', 'VAL':'V', 'GLU': 'E', 'TYR': 'Y', 'MET': 'M','XAA':'X'}

    if len(seq) %3 == 0:
        upper_seq= seq.upper()
        single_seq=''
        for i in range(len(upper_seq)/3):
            single_seq += d[upper_seq[3*i:3*i+3]]
        return single_seq
    else:
        print("ERROR: Sequence was not a factor of 3 in length!")

Answer 6

Biopython has a nice solution

>>> from Bio.PDB.Polypeptide import *
>>> three_to_one('ALA')
'A'

For your example, I'll solve it by this one liner

>>> from Bio.PDB.Polypeptide import *
>>> str3aa = 'ARGHISLEULEULYS'
>>> "".join([three_to_one(aa3) for aa3 in [ "".join(g) for g in zip(*(iter(str3aa),) * 3)]])
>>> 'RHLLK'

They may criticize me for this type of one liner :), but deep in my heart I am still in love with PERL.

Answer 7

Using R:

convert <- function(l) {

  map <- c("A", "R", "N", "D", "C", "E", "Q", "G", "H", "I",
           "L", "K", "M", "F", "P", "S", "T", "W", "Y", "V")

  names(map) <- c("ALA", "ARG", "ASN", "ASP", "CYS", "GLU", "GLN",
                  "GLY", "HIS", "ILE", "LEU", "LYS", "MET", "PHE",
                  "PRO", "SER", "THR", "TRP", "TYR", "VAL")

  sapply(strsplit(l, "(?<=[A-Z]{3})", perl = TRUE),
         function(x) paste(map[x], collapse = ""))
}

convert(c("ARGHISLEULEULYS", "METHISARGARGMET"))
# [1] "RHLLK" "MHRRM"

Answer 8

Another way to do it is with the seqinr and iPAC package in R.

# install.packages("seqinr")
# source("https://bioconductor.org/biocLite.R")
# biocLite("iPAC")

library(seqinr)
library(iPAC)

#read in file
fasta = read.fasta(file = "test_fasta.fasta", seqtype = "AA", as.string = T, set.attributes = F)
#split string
n = 3
fasta1 = lapply(fasta,  substring(x,seq(1,nchar(x),n),seq(n,nchar(x),n)))
#convert the three letter code for each element in the list 
fasta2 = lapply(fasta1, function(x) paste(sapply(x, get.SingleLetterCode), collapse = ""))

# > fasta2
# $`2ppo`
# [1] "RHLLK"
#
# $`3oot`
# [1] "MHRRM"

Answer 9

my %aa_hash=(
  Ala=>'A',
  Arg=>'R',
  Asn=>'N',
  Asp=>'D',
  Cys=>'C',
  Glu=>'E',
  Gln=>'Q',
  Gly=>'G',
  His=>'H',
  Ile=>'I',
  Leu=>'L',
  Lys=>'K',
  Met=>'M',
  Phe=>'F',
  Pro=>'P',
  Ser=>'S',
  Thr=>'T',
  Trp=>'W',
  Tyr=>'Y',
  Val=>'V',
  Sec=>'U',                       #http://www.uniprot.org/manual/non_std;Selenocysteine (Sec) and pyrrolysine (Pyl)
  Pyl=>'O',
);


    while(<>){
            chomp;
            my $aa=$_;
            warn "ERROR!! $aa invalid or not found in hash\n" if !$aa_hash{$aa};
            print "$aa\t$aa_hash{$aa}\n";
    }

Use this perl script to convert triplet aa codes to single letter code.

Answer 10

For those who land here on 2017 and beyond:

Here's a single line Linux bash command to convert protein amino acid three letter code to single letter code in a text file. I know this is not very elegant, but I hope this helps someone searching for the same and want to use single line command.

sed 's/ALA/A/g;s/CYS/C/g;s/ASP/D/g;s/GLU/E/g;s/PHE/F/g;s/GLY/G/g;s/HIS/H/g;s/HID/H/g;s/HIE/H/g;s/ILE/I/g;s/LYS/K/g;s/LEU/L/g;s/MET/M/g;s/ASN/N/g;s/PRO/P/g;s/GLN/Q/g;s/ARG/R/g;s/SER/S/g;s/THR/T/g;s/VAL/V/g;s/TRP/W/g;s/TYR/Y/g;s/MSE/X/g' < input_file_three_letter_code.txt > output_file_single_letter_code.txt

Solution for the original question above, as a single command line:

sed 's/.\{3\}/& /g' | sed 's/ALA/A/g;s/CYS/C/g;s/ASP/D/g;s/GLU/E/g;s/PHE/F/g;s/GLY/G/g;s/HIS/H/g;s/HID/H/g;s/HIE/H/g;s/ILE/I/g;s/LYS/K/g;s/LEU/L/g;s/MET/M/g;s/ASN/N/g;s/PRO/P/g;s/GLN/Q/g;s/ARG/R/g;s/SER/S/g;s/THR/T/g;s/VAL/V/g;s/TRP/W/g;s/TYR/Y/g;s/MSE/X/g' | sed 's/ //g' < input_file_three_letter_code.txt > output_file_single_letter_code.txt

Explanation:

[1] sed 's/.\\{3\\}/& /g' will spllit the sequence. It will add a space after every 3rd letter.

[2] The second ' sed' command in the pipe will take the output of above and convert to single letter code. Add any non-standard residue as s/XYZ/X/g; to this command.

[3] The third ' sed ' command, sed 's/ //g' will remove white-space.

Answer 11

Python 3 solutions.

In my work, the annoyed part is that the amino acid codes can refer to the modified ones which often appear in the PDB/mmCIF files, like

'Tih'-->'A'.

So the mapping can be more than 22 pairs. The 3rd party tools in Python like

Bio.SeqUtils.IUPACData.protein_letters_3to1

cannot handle it. My easiest solution is to use the http://www.ebi.ac.uk/pdbe-srv/pdbechem to find the mapping and add the unusual mapping to the dict in my own functions whenever I encounter them.

def three_to_one(three_letter_code):
    mapping = {'Aba':'A','Ace':'X','Acr':'X','Ala':'A','Aly':'K','Arg':'R','Asn':'N','Asp':'D','Cas':'C',
           'Ccs':'C','Cme':'C','Csd':'C','Cso':'C','Csx':'C','Cys':'C','Dal':'A','Dbb':'T','Dbu':'T',
           'Dha':'S','Gln':'Q','Glu':'E','Gly':'G','Glz':'G','His':'H','Hse':'S','Ile':'I','Leu':'L',
           'Llp':'K','Lys':'K','Men':'N','Met':'M','Mly':'K','Mse':'M','Nh2':'X','Nle':'L','Ocs':'C',
           'Pca':'E','Phe':'F','Pro':'P','Ptr':'Y','Sep':'S','Ser':'S','Thr':'T','Tih':'A','Tpo':'T',
           'Trp':'W','Tyr':'Y','Unk':'X','Val':'V','Ycm':'C','Sec':'U','Pyl':'O'} # you can add more
    return mapping[three_letter_code[0].upper() + three_letter_code[1:].lower()]

The other solution is to retrieve the mapping online (But the url and the html pattern may change through time):

import re
import urllib.request

def three_to_one_online(three_letter_code):
    url = "http://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/" + three_letter_code
    with urllib.request.urlopen(url) as response:
        single_letter_code = re.search('\s*<td\s*>\s*<h3>One-letter code.*</h3>\s*</td>\s*<td>\s*([A-Z])\s*</td>', response.read().decode('utf-8')).group(1)
    return single_letter_code

Here I directly use the re instead of the html parsers for the simplicity.

Hope these can help.