TabError: inconsistent use of tabs and spaces in indentation

[ankita86]

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]

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

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On Apr 26, 2019, at 2:43 PM, ankita86 ***@***.***> 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 — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#4>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AD3L3NOMVZYTCV7BIARAXVLPSNEM5ANCNFSM4HIZPFSA>.

[ankita86]

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]

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

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On Wed 5 Jun, 2019, 8:42 PM asura117, ***@***.***> 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 """ — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#4?email_source=notifications&email_token=AEWHB5I4LBVLTQPAMFQNBD3PY7JUTA5CNFSM4HIZPFSKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODXAA53Y#issuecomment-499125999>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AEWHB5IDLQFGCDU23VS5ZNDPY7JUTANCNFSM4HIZPFSA> .