Parsing FASTA file using class in Python

Question

[mrth]

Hello, I am new to the world of Biopython and Python in general. I am try to parse a fasta file using class. I have got the following code so far:

from itertools import groupby

class OpenFastaFile:
    def __init__(self, path):
        self.path = path
        self._map = {}
        __fasta_sequences = self.__fasta_iter()

    def __str__(self):
        return self._map.__str__()

    def __fasta_iter(self):
        fh = open(self.path)
        faiter = (x[1] for x in groupby(fh, lambda line: line[0] == ">"))
        for header in faiter:
            header = header.__next__()[1:].strip()
            seq = "".join(s.strip() for s in faiter.__next__())
            self._map[header] = seq

of = OpenFastaFile("sample.fa")
print(of)

However, I receive this output:

Traceback (most recent call last):
  File "UniProtFile.py", line 25, in <module>
    of = OpenFastaFile("sample.fa")
  File "UniProtFile.py", line 12, in __init__
    __fasta_sequences = self.__fasta_iter()
  File "UniProtFile.py", line 21, in __fasta_iter
    header = header.__next__()[1:].strip()
AttributeError: 'itertools._grouper' object has no attribute '__next__'

Process finished with exit code 1

My expected output was something along the lines of a dictionary like this: {'name' : 'ACCAGT' , 'name1' : 'ACGGCTA', etc}

Can someone please show me the error of my ways?

[WouterDeCoster]

I would guess that faiter in the following line should be header:

seq = "".join(s.strip() for s in faiter.__next__())

[mrth]

Thanks for replying! Unfortunately, it still gives the same error message.

[Joe]

Is there any reason that you're trying to implement this as a class?

Answer 1

[mrth]

For those wondering, I have solved the problem. I used this code:

from itertools import groupby
class FastaFile:
    def __init__(self, path):
        self.path = path
        self._map = {}
        self.__fasta_iter()
    def __str__(self):
        return self._map.__str__()
    def __fasta_iter(self):
        fh = open(self.path)
        faiter = (x[1] for x in groupby(fh, lambda line: line[0] == ">"))
        for header in faiter:
            header = header.next()[1:].strip()
            seq = "".join(s.strip() for s in faiter.next())
            self._map[header] = seq
ff = FastaFile("sample.fa")
print (ff)

Answer 2

[Matt Shirley]

If you want a fasta file to act like a sequence dictionary, just use pyfaidx:

import pyfaidx
fa = pyfaidx.Fasta("sample.fa")
for key in fa:
  print(key) # sequence name
  print(fa[key]) # sequence object

You'll be using an efficient method that doesn't read all of your sequences into memory unless you access them.

[mrth]

Thanks for this information. I never knew pyfaidx existed.

Answer 3

[Pallab Bhowmick]

Hi you can try my following code to generate your result:

   from Bio import SeqIO
      seqdic={}
       with open('sample.fa', 'r') as input_fasta_file:
            for seq_record in SeqIO.parse(input_fasta_file, 'fasta'):
                header = seq_record.id
                seqs = str(seq_record.seq)
                seqdic[header]=seqs
  

[WouterDeCoster]

As a comment: SeqIO.parse also takes a filename as input, not necessarily a file handle. So you could do

for seq_record in SeqIO.parse('sample.fa', 'fasta'):

You could also "simplify" your code using a dict comprehension, faster and more concise.

seqdic={seq_record.id: str(seq_record.seq) for seq_record in SeqIO.parse('sample.fa', 'fasta')}

[st.ph.n]

I was going to post a code similar to this, but the OP's question seemed as if it was an assignment because it is overly complicated.

[mrth]

You were correct. It is for an assignment. I usually use with open to parse my files but need to try something new this time around - classes.

[mrth]

Hi there, I really appreciate the response! However, I'm trying to use class with magic methods to parse it as I need to add it somewhere within my code (for an assessment). I feel as though I am really close but yet so far away!