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Making my python code better

Hi,

I am looking for a way to make my current python code better. I am not advanced in python as I am a biologist.

Is there some way to make an if statement that reads if each line for my file starts with "+" or "-" and thus make a graph as blue and yellow per condition ? Basically the "+" or "-" for each line are prefixes for genes contained or not contained in my lists of interest.

I have no idea how could I even start this so yeah if you are python advanced and feel like helping me I would appreciate it.

for example

file_1.txt = AAAS,ACTB,LIMS1
file_2.txt = AAAS,ACTN4,ACTN1
if file_1> file_2
  print("The genes that differ are:")
  plot  (volacno plot, yellow dots)
elif file_1 == file_2:
  print("The common genes are:")
  plot  (volacno plot, blue dots)

thanks

python
• 1,915 views • link
written by ciaki • ciaki

I do not have a code because i have no idea how to achieve this. The input is two gene files. and i am comparing the genes between the two files. my question is how to format the if statement for that.

• 0 views • link
written by ciaki • ciaki

Realistically nobody is going to want to / be able to help you unless they see some code and data, that's a minimum really.

• 0 views • link
written by 4galaxy77 4galaxy77

Show us the sample input (the content of two files) and the desired output.

• 0 views • link
written by Andrzej Zielezinski Andrzej Zielezinski

I updated the initial comment with an example

• 0 views • link
written by ciaki • ciaki

1 answer

well, I know you're learning python, but this simple task is usually performed using bash. This is basic linux, really.

# replace comma with carriage returns, sort , keep the unique names
tr "," "\n" < file_1.txt | sort | uniq > genes1.txt
tr "," "\n" < file_2.txt | sort | uniq > genes2.txt


# common genes
comm -12 genes1.txt genes2.txt

# unique in 1
comm -23 genes1.txt genes2.txt


# unique in 2
comm -13 genes1.txt genes2.txt
• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

Thanks Pierre. I have actually done it before using bash commands but it does not sort out the fact that i am hoping to create a graph for this. But thank you for your input.

• 0 views • link
written by ciaki • ciaki

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