Running python in the terminal, syntax error

Question

I'm trying to run a python program in the terminal. I have successfully called the .py script using python filename.py, and once the script starts running it asks for the first input file, which is a .csv file. When I type the path to that .csv file, I get a syntax error. See below for all the code starting with calling the python script.

python /Users/juliafiske/Desktop/GTSeq_Pipeline/Genotyping_Scripts/Genotyping_Scripts/GTseq_BarcodeSplit_MP_NextSeq_10K.py 

type the path to input file
Format= /home/user/...

/Users/juliafiske/Desktop/GTSeq_Pipeline/Practice/Practice_sampleIDs_new.csv
Traceback (most recent call last):
  File "/Users/juliafiske/Desktop/GTSeq_Pipeline/Genotyping_Scripts/Genotyping_Scripts/GTseq_BarcodeSplit_MP_NextSeq_10K.py", line 24, in <module>
    path1 = input()
  File "<string>", line 1
    /Users/juliafiske/Desktop/GTSeq_Pipeline/Practice/Practice_sampleIDs_new.csv
    ^
SyntaxError: invalid syntax

The beginning of the .py script being called looks like this:

from multiprocessing import Process

print('type the path to input file\nFormat= /home/user/...')
path1 = input()

print('type the path to the fastq file to split\nFormat= /home/user/...')
path2 = input()

That worked!! Thank you so much. Such a simple fix, I'm a beginner! — Aviva
– Aviva, Commented Dec 4, 2019 at 23:08

John Gordon · Accepted Answer · 2019-12-04 22:52:22Z

3

You're using Python 2.

Use raw_input() instead of input() to collect keyboard input.

answered Dec 4, 2019 at 22:52

John Gordon

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Comments

Aviva · Accepted Answer · 2019-12-04 23:09:57Z

1

Quotations were needed around /Users/juliafiske/....

answered Dec 4, 2019 at 23:09

Aviva

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