Text files¶

Python has strong function to work with file and folders.

Manipulating¶

To access a text file in Python, you need to: 1) open the file, 2) read\write it, and 3) close the file.

Write¶

The following code creates a new file and writes text to it; if the file already exists, it will be overwritten

test = open("example.txt", "w")
for i in range(0,10):
    test.write(f"add {i}\n")
test.close()

As you can see here we use 'w' mode, which means Write-only. Overwrites file if it exists; creates new if it doesn’t.

Lines can be added easily to file.

lines = ['first line\n', 'second line\n']
open('my_file.txt','w').writelines(lines)

Table can be added to file as below:

names = ['Emily', 'Bob', 'Charlie']
ages = [23, 45, 67]

f = open('my_file.txt', 'w')
for name, age in zip(names, ages):
    line = f'{name};{age}\n'
    f.write(line)
f.close()

Append¶

To append new line use a mode, you can use .write() or writelines():

test = open("example.txt", "a")  # append mode
test.write("Today \n")
test.close()

test = open("example.txt", "a")
L = ["This is just example Delhi \n", "in Python \n"]
test.writelines(L) 
test.close()

Read¶

The entire file can be viewed using the following code; as you can see, we use the 'r' mode.

test = open("example.txt", "r")
print(test.read())
test.close()

The entire file can be read in a file

f = open('example.txt')
text = f.read()
f.close()

You can access each line of the file element by element as follows:

with open("example.txt", "r") as handle:
    for line in handle:
        print(line.strip())

with open("example.txt", "r") as handle:
    print(handle.read())

In Python, the next() function is used to retrieve the next item from an iterator.

handle = open("example.txt", "r")
line = next(handle)
print(line)    
line = next(handle)
print(line)

If the columns are separated using ;, the file can be separated as

for line in open('my_file.txt'):
    columns = line.strip().split(';')
    first = columns[0]
    last = columns[1]
    age = int(columns[2])

If the file in not in the directory folder, you can recall it

import os
p = os.path.join('/home/ubuntu', 'data.csv')

with open(p) as fp:
    data = fp.read()

Online file¶

A simple way to access to a file online is to use urllib module,

import urllib.request
url = "https://raw.githubusercontent.com/ucdavis-bioinformatics-training/2020-Bioinformatics_Prerequisites_Workshop/master/Intro_to_Python/example_data.fastq.gz"
urllib.request.urlretrieve(url, 'example_data.fastq.gz')

import os
# to check whether file is in the working path
os.path.isfile("example_data.fastq.gz")
# to check the size of file
os.path.getsize("example_data.fastq.gz")

zip file¶

To handle the zip file, use the gzip module, as shown below.

import gzip
handle = gzip.open("example_data.fastq.gz", 'rt')
l = next(handle)
print(l)
handle.close()

table¶

If the data is saved as table, use pd.read_table,

users = pd.read_table('https://raw.githubusercontent.com/justmarkham/DAT8/master/data/u.user', sep='|', index_col='user_id')
users.head()