search

jpiper / pyDNase

Python module for the easy handling and analysis of DNase-seq data
http://jpiper.github.io/pyDNase
MIT License
37 stars 24 forks source link

Error in wellington_footprints.py when reading bed file #36

Closed KRSBar closed 6 years ago

KRSBar commented 6 years ago

Hello,

I get the following error when trying to run wellington_footprints.py:

File "/home/barnekr1/.conda/envs/pydnase/bin/wellington_footprints.py", line 86, in orderedbychr = [item for sublist in sorted(regions.intervals.values()) for item in sorted(sublist, key=lambda peak: peak.startbp)] TypeError: '<' not supported between instances of 'GenomicInterval' and 'GenomicInterval'

This is running: pydnase 0.2.6 python 3.6.2

Installation was done in an anaconda virtual environment with: conda install -c bioconda pydnase

I am able to successfully run example_footprint_scores.py.

I believe this may be the same issues #35 addressed by @dpryan79 Should this fix work? Can these changes simply be manually made to files or is a fresh installation needed? Any advice is appreciated.

jpiper commented 6 years ago

Hey there. I need to merge that PR and push out a new version to PyPi. I hope to get around to it this weekend!

KRSBar commented 6 years ago

Thanks for yours and @dpryan79 's efforts! I'm hoping this resolves my issue.

KRSBar commented 6 years ago

I went ahead and manually did the reinstall with the new merged fix. Everything seems to have ran smoothly!

jpiper commented 6 years ago

Fantastic!