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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

Python 3 regression in `wellington_footprints.py` #22

Closed jpiper closed 6 years ago

jpiper commented 7 years ago

The core scripts needs to be tested on Python 3 as well, some of them don't work...

Traceback (most recent call last):
  File "/n/data2/bch/surg/hla/PMA_analysis_final/new_pyDNase/venv/bin/wellington_footprints.py", line 70, in xrange_from_string
    range_string = range(range_string[0],range_string[1],range_string[2])
TypeError: 'map' object is not subscriptable

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/n/data2/bch/surg/hla/PMA_analysis_final/new_pyDNase/venv/bin/wellington_footprints.py", line 77, in <module>
    clargs.shoulder_sizes = xrange_from_string(clargs.shoulder_sizes)
  File "/n/data2/bch/surg/hla/PMA_analysis_final/new_pyDNase/venv/bin/wellington_footprints.py", line 74, in xrange_from_string
    raise ValueError
ValueError

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/n/data2/bch/surg/hla/PMA_analysis_final/new_pyDNase/venv/bin/wellington_footprints.py", line 80, in <module>
    raise RuntimeError("shoulder and footprint sizes must be supplied as from,to,step")
RuntimeError: shoulder and footprint sizes must be supplied as from,to,step