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michael-weinstein / autoIGV

This program can take a tab-delimited text file containing bam file paths and loci and create a subdirectory of image captures for you.
MIT License
2 stars 1 forks source link

Not able to run autoIGV1.5.py! #5

Closed Eteleeb closed 4 years ago

Eteleeb commented 4 years ago

HI Michael,

I am trying to use your autoIGV tool but I am receiving this error

 File "autoIGV1.5.py", line 241
    def await(igv, expectedresponse = ''):  #the second argument here is optional, and is only going to be supplied if the goal is to get a specific response from IVG (probably echo).  IGV usually responds "OK" when a command is completed or with Error:(Message) when a command fails.
            ^
SyntaxError: invalid syntax

I am not sure what is missing. I did follow all instructions as you posted. Is this because of a different version of python?. I am using python3.7. Any help will be appreciated.

Thank you.

-Abdallah

michael-weinstein commented 4 years ago

Python 3.7 is definitely not the version of python I initially made this for, but I don't think that should be the issue here. I didn't realize people were still using this.

Having just run a quick google search, I know what the issue is: await was previously nothing special, but with python trying to add in better support for async operations, await became a reserved word. With 3.4 (which is what I wrote this on) that was not an issue. With enhanced async functionality, my function name is now a reserved word.

Gimme a minute.

michael-weinstein commented 4 years ago

Ok, did some cleanup on the file and renamed the function and its references. Please try using the current version and let me know if this resolves it.

I guess I should probably clean up this code a bit if people are still using it.

Out of curiosity, what are you using this program for/what are you studying?

Eteleeb commented 4 years ago

Thank you so much. Will try and let you know.

As part of our QC analyses, we perform a variant checking analysis where we look at a number of variants in a number of samples (usually > 100). Most of our studies are related to Alzheimer's disease.

Thank you.

-A