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girirajanlab / CN_Learn

CN-Learn
GNU General Public License v3.0
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annotate_window.sh buggy #9

Open martiliasf opened 4 years ago

martiliasf commented 4 years ago

I had to place this line in this file for it to run

source /path/to/config.params

I also get this error:

File "/pine/scr/m/a/martyf/cn-learn/CN_Learn/software/clamms//calc_window_mappability.py", line 69 print "%s\t%d\t%d%s\t%.3f" % (window[0], window[1], window[2], window[3], ^ SyntaxError: invalid syntax Job ended on c0315.ll.unc.edu at Mon Jan 6 14:46:25 EST 2020

carrot points to the " in .3f" in terminal

martiliasf commented 4 years ago

I fixed this with the following modification. I can't make a PR because the file is packed up in a tarball. 

print ("%s\t%d\t%d%s\t%.3f" % (window[0], window[1], window[2], window[3],
                              tot_val/tot_bp if tot_bp > 0 else 0.0))
girirajanlab commented 4 years ago

Unfortunately, this particular script is part of the prepackaged CLAMMS pipeline. We chose not to modify scripts that were part of the callers we used. This particular script and pipeline was tested at least twice during development, so the error is a bit of a surprise. Could you please clarify what you mean by PR?

martiliasf commented 4 years ago

pull request to your codebase to fix the problem.