How do I use data from one function in another function in python?

Question

Hello I am pretty new to python and I want to do the following:

I have a function that opens a file, reads the file, closes the file and returns the data:

def getFastaFromFile(filename):
    """ Read a fasta file (filename) from disk and return
    its full contents as a string"""
    inf=open(filename)
    data=inf.read()
    inf.close()
    return data

The data that is being returned are a few lines with strings.

What I want to do is have another function that uses the data from the first function and perform the .readlines(), .readline() and .count() commands

My second function:

def printTableFromFasta(fastarec):
    a= data.readlines()
    for i in range(a)
        b= data.readline()
        c= b.count('A')
        print(c)

As output I would like to print the amount of times string "A" appears for every line from the data. The problem I get with this code is that the data doesn't get recognized.

Fruity Medley · Accepted Answer · 2019-12-03 21:46:39Z

1

First, you need to pass the data you are wanting to read into the second function, like so

def printTableFromFasta(data):

In order to get this from your first function, try returning the entire contents of the file

def getFastaFromFile(filename):
    with open(filename, 'r') as inf: # handles open and close
        data = inf.readlines()       # Returns the entire file as a list of strings
    return data

Your function call will look something like this

printTableFromFasta(getFastaFromFile(filename))

Then, in your second function, you don't need to call readlines, it's already a list.

def printTableFromFasta(data):
    for line in data            # look at each line
        print(line.count('A'))  # count 'A'

Edit: To only read from the second function and not touch the first function

def printTableFromFasta(filename):
    with open(filename, 'r') as inf: # handles open and close
        for line in inf.readlines()  # look at each line
            print(line.count('A'))   # count 'A'

edited Dec 3, 2019 at 21:46

answered Dec 3, 2019 at 21:30

Fruity Medley

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3 Comments

NN28 Over a year ago

Thank you Groger, this works, but is there a way to do this without changing the first function? I only want to do the reading commands in the second function.

Fruity Medley Over a year ago

@NawinNarain The file closes when getFastaFromFile ends. If you only want to change the second function, I can make an edit, but it involves only using the second function.

NN28 Over a year ago

Thank you for the edit Groger! This is what I needed!

FBB · Accepted Answer · 2019-12-03 21:40:13Z

Remember that the data variable in the first function is local. It cannot be accessed from outside the function it is defined in.

For example, the getName() function returns a variable which is locally called data but you access the value by calling the function.

def getName(user_id):
    data = "Your name is " + str(user_id)
    return data 

# Throws an error, because data in undefined 
name = getName("Bobby")
print(data)

# Working code, prints "Your name is Bobby"
name = getName("Bobby")
print(name)

There are no rules against calling one function from inside another. Instead of a = data.readlines() try a = getFastaFromFile("dna.fasta') as well as changing data = inf.read() to data = inf.readlines()

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