Chris_Rands Chris_Rands - 4 months ago 14
Python Question

Reading in file block by block using specified delimiter in python

I have an input_file.fa file like this (FASTA format):

> header1 description
data data
data
>header2 description
more data
data
data


I want to read in the file one chunk at a time, so that each chunk contains one header and the corresponding data, e.g. block 1:

> header1 description
data data
data


Of course I could just read in the file like this and split:

with open("1.fa") as f:
for block in f.read().split(">"):
pass


But I want to avoid the reading the whole file into memory, because the files are often large.

I can read in the file line by line of course:

with open("input_file.fa") as f:
for line in f:
pass


But ideally what I want is something like this:

with open("input_file.fa", newline=">") as f:
for block in f:
pass


But I get an error:


ValueError: illegal newline value: >


I've also tried using the csv module, but with no success.

I did find this post from 3 years ago, which provides a generator based solution to this issue, but it doesn't seem that compact, is this really the only/best solution? It would be neat if it is possible to create the generator with a single line rather than a separate function, something like this pseudocode:

with open("input_file.fa") as f:
blocks = magic_generator_split_by_>
for block in blocks:
pass


If this is impossible, then I guess you could consider my question a duplicate of the other post, but if that is so, I hope people can explain to me why the other solution is the only one. Many thanks.

Answer

A general solution here will be write a generator function for this that yields one group at a time. This was you will be storing only one group at a time in memory.

def get_groups(seq, group_by):
    data = []
    for line in seq:
        # Here the `startswith()` logic can be replaced with other
        # condition(s) depending on the requirement.
        if line.startswith(group_by):
            if data:
                yield data
                data = []
        data.append(line)

    if data:
        yield data

with open('input.txt') as f:
    for i, group in enumerate(get_groups(f, ">"), start=1):
        print ("Group #{}".format(i))
        print ("".join(group))

Output:

Group #1
> header1 description
data data
data

Group #2
>header2 description
more data
data
data

For FASTA formats in general I would recommend using Biopython package.