eivindgl
commented
7 years ago Thank you for notifying me. The issue was a non backwards compatible change in the Pandas library EDD depends on. I have updated EDD and version 1.1.18 works with the most recent pandas version.
run pip install -U edd to upgrade
runningvato
Hello,
Edd runs to completion when I specify a gap penalty score, but hangs up with the following error when I don't specify a gap penalty:
Traceback (most recent call last): File "/usr/local/bin/edd", line 146, in
main(args, config)
File "/usr/local/bin/edd", line 69, in main
df = loader.get_df(args.unalignable_regions.name)
File "/usr/local/lib/python2.7/dist-packages/eddlib/experiment.py", line 201, in get_df
mc_trials=100, pval_lim=0.05)
File "/usr/local/lib/python2.7/dist-packages/eddlib/estimate.py", line 89, in instantiate
util.save_bin_score_file(binscore_df, bedgraph_path)
File "/usr/local/lib/python2.7/dist-packages/eddlib/util.py", line 10, in save_bin_score_file
df['chrom start end score'.split()].sort(['chrom', 'start']).to_csv(
File "/usr/local/lib/python2.7/dist-packages/pandas/core/generic.py", line 3081, in getattr
return object.getattribute(self, name)
AttributeError: 'DataFrame' object has no attribute 'sort'
All dependencies were up-to-date and installed prior to installing Edd. Any ideas on what to do?
Thanks for your time!