How to convert Protein sequence to one hot encoding in python?

Question

I use this code to one-hot encoding my sequences but it just works for a single sequence and doesn't work for my CSV file which contains my sequences, what can I do for that? this is code

data = 'MGILPSPGMPALLSLVSLLSVLLMGCVAETGTQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNEVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPSGAGSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKGSGRENLYFQGGGGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGHHHHHHHH'

alphabet = ['A', 'C', 'D', 'E', 'F', 'G','H', 'I', 'K', 'L', 'M', 'N', 'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'Y']

char_to_int = dict((c, i) for i, c in enumerate(alphabet))

integer_encoded = [char_to_int[char] for char in data]

onehot_encoded = list()
for value in integer_encoded:
    letter = [0 for _ in range(len(alphabet))]
    letter[value] = 1
    onehot_encoded.append(letter)

e = np.array(onehot_encoded)

this code is working for a single sequence but when I want to use my whole dataset which is a CSV file, it does not work.

data = pd.read_csv("database.csv", usecols=[4])

and this is my database.csv looks like and this is column[4]

    Sequence
0   MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSS...
1   MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSS...
2   MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSS...
3   MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSS...
4   MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSS...
5   MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSS...
6   MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSS...
7   MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSS...
8   MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSS...
.
.
.
40  MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSS...
41  MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSS...
42  MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSS...
43  MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSS...
44  MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSS...
45  MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSS...

and this is the error

---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
in <module>
      5 char_to_int = dict((c, i) for i, c in enumerate(alphabet))
      6 
----> 7 integer_encoded = [char_to_int[char] for char in data]
      8 
      9 onehot_encoded = list()


      5 char_to_int = dict((c, i) for i, c in enumerate(alphabet))
      6 
----> 7 integer_encoded = [char_to_int[char] for char in data]
      8 
      9 onehot_encoded = list()

KeyError: 'Sequence'

and this is the error after using this code

# Import Dependencies 
import pandas as pd
import numpy as np

# Function to encode sequences
def encode_seq(sequence):
    alphabet = ['A', 'C', 'D', 'E', 'F', 'G','H', 'I', 'K', 'L', 'M', 'N', 'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'Y']
    char_to_int = dict((c, i) for i, c in enumerate(alphabet))
    integer_encoded = [char_to_int[char] for char in data]
    onehot_encoded = list()

    for value in integer_encoded:
        letter = [0 for _ in range(len(alphabet))]
        letter[value] = 1
        onehot_encoded.append(letter)

    return np.array(onehot_encoded)


# Read .csv
df = pd.read_csv('database.csv')

# Keep only Sequence column
df = df.filter(['Sequence'])

# Create a new column Encoded_Sequences containing encoded sequences from Sequence column
df['Encoded_Sequences'] = df['Sequence'].apply(lambda x: encode_seq(x))

KeyError                                  Traceback (most recent call last)
 in <module>
     25 
     26 # Create a new column Encoded_Sequences containing encoded sequences from Sequence column
---> 27 df['Encoded_Sequences'] = df['Sequence'].apply(lambda x: encode_seq(x))

 in apply(self, func, convert_dtype, args, **kwargs)
   4355         dtype: float64
   4356         """
-> 4357         return SeriesApply(self, func, convert_dtype, args, kwargs).apply()
   4358 
   4359     def _reduce(

 in apply(self)
   1041             return self.apply_str()
   1042 
-> 1043         return self.apply_standard()
   1044 
   1045     def agg(self):

 in apply_standard(self)
   1097                 # List[Union[Callable[..., Any], str]]]]]"; expected
   1098                 # "Callable[[Any], Any]"
-> 1099                 mapped = lib.map_infer(
   1100                     values,
   1101                     f,  # type: ignore[arg-type]

 in pandas._libs.lib.map_infer()

 in <lambda>(x)
     25 
     26 # Create a new column Encoded_Sequences containing encoded sequences from Sequence column
---> 27 df['Encoded_Sequences'] = df['Sequence'].apply(lambda x: encode_seq(x))

 in encode_seq(sequence)
      7     alphabet = ['A', 'C', 'D', 'E', 'F', 'G','H', 'I', 'K', 'L', 'M', 'N', 'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'Y']
      8     char_to_int = dict((c, i) for i, c in enumerate(alphabet))
----> 9     integer_encoded = [char_to_int[char] for char in data]
     10     onehot_encoded = list()
     11 

 in <listcomp>(.0)
      7     alphabet = ['A', 'C', 'D', 'E', 'F', 'G','H', 'I', 'K', 'L', 'M', 'N', 'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'Y']
      8     char_to_int = dict((c, i) for i, c in enumerate(alphabet))
----> 9     integer_encoded = [char_to_int[char] for char in data]
     10     onehot_encoded = list()
     11 

KeyError: 'Sequence'

I need to multiply to another matrix so I need to one-hot encode them and turn them to Numpy array but it doesn't work with this code so what should I do?

Answer 1

# Import Dependencies 
import pandas as pd
import numpy as np

# Function to encode sequences
def encode_seq(sequence):
  alphabet = ['A', 'C', 'D', 'E', 'F', 'G','H', 'I', 'K', 'L', 'M', 'N', 'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'Y']
  char_to_int = dict((c, i) for i, c in enumerate(alphabet))
  integer_encoded = [char_to_int[char] for char in sequence]
  onehot_encoded = list()

  for value in integer_encoded:
      letter = [0 for _ in range(len(alphabet))]
      letter[value] = 1
      onehot_encoded.append(letter)

  return np.array(onehot_encoded)


# Read .csv
df = pd.read_csv('database.csv')

# Keep only Sequence column
df = df.filter(['Sequence'])

# Create a new column Encoded_Sequences containing encoded sequences from Sequence column
df['Encoded_Sequences'] = df['Sequence'].apply(lambda x: encode_seq(x))