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zavolanlab / PAQR_KAPAC

scripts, pipelines and documentation to run PAQR and KAPAC; KAPAC allows to infer regulatory sequence motifs implicated in 3’ end processing changes; PAQR enables the quantification of poly(A) site usage from standard RNA-seq data
GNU General Public License v2.0
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Incorrect indentation in one of the scripts. #7

Open AngryMaciek opened 4 years ago

AngryMaciek commented 4 years ago

My initial problem is that I want to run PAQR with Python3. While I was modifying the syntax in the scripts I noticed a piece of code that did not raise any error while running with Python2, hovewer with Python3 - it does: IndentationError: expected an indented block. I nailed the error down: please take a look at the script deNovo-used-sites-and-usage-inference.single_distal_included.py, lines 1650:1678 in this repository. Tabs are mixed with spaces and I cannot disentangle how the proper indentation should look like.
I have been trying and guessing a few options (with an input that I know that runs through on Python2) but all of them resulted in another error downstream.

fgypas commented 4 years ago

Hi @koljaLanger

Can you please take a look on it. When I clone the repo indeed there is an indentation issue with this file.

Thank you in advance

Best Foivos

AngryMaciek commented 4 years ago

In my case I have resolved the issue with a substitution: 1TAB -> 8SPACES. But I think you should still correct this repository and test run it. Maciek

koljaLanger commented 4 years ago

Many thanks for the report! I updated the script and uploaded a revised version. Ralf