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mhguo1 / TRAPD

Burden testing against public controls
MIT License
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TabError: inconsistent use of tabs and spaces in indentation #4

Open ankita86 opened 5 years ago

ankita86 commented 5 years ago

Hi, I am trying to use your codes for analysis. Unfortunately, with every code I am getting this indentation error. Please suggest how to resolve. I have installed required packages. Also, it looks like operator and optparse are depreciated.

Thanks, Ankita

mhguo1 commented 5 years ago

Hi Ankita, Apologies for the delayed response. I'm not sure why you are getting an indentation error. I've been able to run it just fine as have a number of people I've spoken to. Did you clone TRAPD directly from GitHub? What version of Python are you using?

Yes, I am aware that optparse is deprecated and I do have plans to update TRAPD to not use optparse in the near future.

Thank you, Michael

On Apr 26, 2019, at 2:43 PM, ankita86 notifications@github.com wrote:

Hi, I am trying to use your codes for analysis. Unfortunately, with every code I am getting this indentation error. Please suggest how to resolve. I have installed required packages. Also, it looks like operator and optparse are depreciated.

Thanks, Ankita

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ankita86 commented 5 years ago

Hi Michael,

Thanks for your reply.

Now, my issue has been resolved. I am trying to use TRAPD with python 3 and therefore, I was getting this error. When I used python 2.7 and configured pybedtools with the same then I didn't get any error.

ankita86 commented 5 years ago

Using python2. 7 as well as configuring pybed tools with python2. 7 solved my issue.

On Wed 5 Jun, 2019, 8:42 PM asura117, notifications@github.com wrote:

Hi Michael, I am getting the same error... """ module load python/2.7.11 module load pybedtools/0.7.8

python make_snp_file.py -v filt_merged_leftaligned_single.vep.vcf --vep -o snpfile.txt --genecolname SYMBOL --excludevep "CADD_PHRED[<]15" --excludevep "gnomaADg_non_cancer_AF_nfe[>]0.001" --snpformat "CHRPOSREFALT" --bedfile manifest2.bed --pass --genenull """

File "make_snp_file.py", line 48 parser.error('--vep option must be supplied if using VEP annotations') ^ IndentationError: expected an indented block """

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