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gstecher / CloneFinderAPI

API for the Clone Finder application
MIT License
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NameError: name 'params' is not defined #3

Open ahorn720 opened 4 years ago

ahorn720 commented 4 years ago

from /Users/ahorning/CloneFinderAPI/clonefinder

I ran python clonefinder.py snv /Users/ahorning/Google Drive/Stanford_postdoc/Research/FAP Samples_EdEsplin/DNAseq_WGS/scripts/RupingPipelineLocalCopies/post-VAP/Bulk_A001_A002/clonefinder/A001_HETsegmentsonly.txt

and got this error: 2019-12-10 12:56:13.751637 loading config file: options.ini config parameters loaded successfully parsing command-line parameters... Errors in options.ini Traceback (most recent call last): File "clonefinder.py", line 37, in <module> parser.input_data_file = params.input_data_file NameError: name 'params' is not defined

Im not sure what went wrong...

ahorn720 commented 4 years ago

I should mention that when I tried using the example input file... it seems to work just fine.

ahorn720 commented 4 years ago

the only things I can tell that are different between the example file and mine are that I've filled my SNVID column with items like the following: `

SNVID
chr1:1048090:rs747114622:C:T
chr1:1128169:.:T:C
chr1:1240555:.:A:C
chr1:1459342:.:G:A
chr1:1530556:rs186520555:G:A
SayakaMiura commented 4 years ago

The problem is that there is a space in the path to your input file. Please try: python clonefinder.py snv "/Users/ahorning/Google Drive/Stanford_postdoc/Research/FAP Samples_EdEsplin/DNAseq_WGS/scripts/RupingPipelineLocalCopies/post-VAP/Bulk_A001_A002/clonefinder/A001_HETsegmentsonly.txt" If you still get the same error, please move your input file from the Google Drive into your PC.

ahorn720 commented 4 years ago

Thank you very much for your help. You helped me figure out that there was certainly something wrong with my input file.

Turns out, I had quotes in my input file I didn't realize. I fixed this by using the write.table(..., quote = FALSE) argument in my R code.

Its running now so hopefully it works :)