how to re-arrange 3 for loops in a script to be just one

Question

I have this script that contains four different function. Function 2-4 have a common path, the for loop. I would like to get some help so I can sort that 'for loop' making it into one but depending on the function to get the data from the right file, fastqs, faster or xml.

> def One(): #gene extraction
    #do something
One()

def Two(path_to_folder_H*,something_else): # de novo assembly
    #do something with files

folders=glob.glob(path_to_folder_H*)
for folder in folders:
    my_file=glob.glob(file.fastqs)
    if folder exit:
       #do something
    elif:
        # do something else
   Two(path_to_folder_H*,something_else)

def Third(path_to_folder_H*, someting_else_2): #database+blast
    #do something

folders=glob.glob(path_to_folder_H*)
for folder in folders:
    my_file=glob.glob(file.fa)
    Third(path_to_folder_H*,something_else_2)

def Fouth(path_to_folder_H*,something_else_3): #parsing file
    #do someething
count=0
dict={}
folders=glob.glob(path_to_folder_H*)
for folder in folders:
    my_file=glob.glob(file.xml)
    if something:
           #do something
    elif:
   #something else
    Fourth(path_to_folder_H*,something_else_3)

This code is about 200 line long, and I just put a synopsis to abbreviate. The first function extract data from a file. The second function does the novo assembly with the fastqs file, and give a confing.fa. The third function uses the cotings.fa and a file obtained with the first function to do a database, and blast, giving an xml file. The fourth function parse the xml obtained with the third funcion.

The question title doesn't appear to match the content. What exactly are you trying to do? — roganjosh, Jul 12 '17 at 12:06
Answering the title: [Duplicate](https://stackoverflow.com/questions/19201290/how-to-save-a-dictionary-to-a-file). But I assume, you want to do something else? — P. Siehr, Jul 12 '17 at 12:08
You are absolutely right. That is for another question I wanted to ask but I found the solution. I am going to change it. Thanks for letting me know. — Ana, Jul 12 '17 at 12:09
So with the updated title, all you have to do is move some code around. Define your functions at the top, copy/paste the code that's currently across 3 `for` loops into a single `for folder in folders`. Did you try this? What is your blocker - do you get errors? — roganjosh, Jul 12 '17 at 12:12

P. Siehr · Accepted Answer · 2017-07-12T12:45:21.170

1

With the latest edits of the question, I edited this answer as well. You can simply define the functions at the top of your Python-script. Using your code this would look like the following:

def One():
    # do one

def Two(path_to_folder_H*,something_else):
    #do something with files

def Third(path_to_folder_H*, someting_else_2):
    #do something with files

def Fouth(path_to_folder_H*,something_else_3):
    #do someething with files

# -- main -- 

One()
folders=glob.glob(path_to_folder_H*)

for folder in folders:

    my_file=glob.glob(file.fastqs)
    Two(path_to_folder_H*,something_else)

    my_file=glob.glob(file.fa)
    Third(path_to_folder_H*,something_else_2)

    my_file=glob.glob(file.xml)
    Fourth(path_to_folder_H*,something_else_3)

edited Jul 12 '17 at 12:45

answered Jul 12 '17 at 12:15

P. Siehr

525
1
6
22

I added some explanation to make it clear. Hope it helps. – Ana Jul 12 '17 at 12:30
Ok, I understand that they should be executed one after another. So why not use the third code part in this answer? – P. Siehr Jul 12 '17 at 12:32
P.Siehr, I tried what you suggested, which it is good but I have a few 'if and else' underneath my_files. I have updated the code for guidance, and understanding on what I am saying. – Ana Jul 12 '17 at 13:27
@Ana To be honest, I don't see any problem. Can you provide a [minimal working example](https://stackoverflow.com/help/mcve)? – P. Siehr Jul 12 '17 at 14:32
The error message I get is about that the second my_file does not match indentation. So I have to check the script, and see the problem. It must be about one space indentation. But I agree with you that you example code should work. – Ana Jul 12 '17 at 15:19

how to re-arrange 3 for loops in a script to be just one

1 Answers1