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Shamir-Lab / Recycler

This is the codebase for Recycler, described in our manuscript: https://academic.oup.com/bioinformatics/article/33/4/475/2623362, by Roye Rozov, Aya Brown Kav, David Bogumil, Naama Shterzer, Eran Halperin, Itzhak Mizrahi, and Ron Shamir
BSD 3-Clause "New" or "Revised" License
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AttributeError: Digraph object #44

Closed vappiah closed 3 years ago

vappiah commented 3 years ago

Hi @dpellow

I tried running the recycler with the command below and I got an error. Please advice

_recycle.py -g assemblygraph.fastg -k 50 -b ".mybam -o mydir

Error message 143.506632 6899.693496211945 258.95512825000003 Traceback (most recent call last): File "/home/user/.local/bin/recycle.py", line 4, in import('pkg_resources').run_script('recycler==0.62', 'recycle.py') File "/opt/apps/Python/Python-3.5/lib/python3.5/site-packages/pkg_resources/init.py", line 658, in run_script self.require(requires)[0].run_script(script_name, ns) File "/opt/apps/Python/Python-3.5/lib/python3.5/site-packages/pkg_resources/init.py", line 1445, in run_script exec(script_code, namespace, namespace) File "/home/user/.local/lib/python3.5/site-packages/recycler-0.62-py3.5.egg/EGG-INFO/scripts/recycle.py", line 100, in File "/home/user/.local/lib/python3.5/site-packages/recycler-0.62-py3.5.egg/recyclelib/utils.py", line 205, in get_long_self_loops AttributeError: 'DiGraph' object has no attribute 'nodes_with_selfloops'

dpellow commented 3 years ago

It's hard to tell without knowing more - how was Recycler installed? It looks like it is using Python3 even though Recycler is written in Python2. It seems like the problem is with the version of NetworkX - which version did you install?

By the way, we now recommend to use our new tool SCAPP instead of Recycler.