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?
•
written
by
mrth •
3 answers
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)
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.
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
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')}
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I would guess that
faiterin the following line should beheader:Thanks for replying! Unfortunately, it still gives the same error message.
Is there any reason that you're trying to implement this as a class?