search

BinPro / CONCOCT

Clustering cONtigs with COverage and ComposiTion
Other
119 stars 48 forks source link

'DataFrame' object has no attribute 'ix' #289

Open Naima16 opened 4 years ago

Naima16 commented 4 years ago

Hello

I am running concoct command: concoct --composition_file contigs_10K.fa --coverage_file coverage_table.tsv -b concoct_output/**

which generate this error:

Up and running. Check /lustre03/project/6006375/naima17/oral_microbiome/binning_concoct/concoct_output/log.txt for progress Traceback (most recent call last): File "/home/naima17/virtual_env/Concoct/bin/concoct", line 4, in import('pkg_resources').run_script('concoct==1.0.0', 'concoct') File "/home/naima17/virtual_env/Concoct/lib/python3.7/site-packages/pkg_resources/init.py", line 666, in run_script self.require(requires)[0].run_script(script_name, ns) File "/home/naima17/virtual_env/Concoct/lib/python3.7/site-packages/pkg_resources/init.py", line 1453, in run_script exec(code, namespace, namespace) File "/home/naima17/virtual_env/Concoct/lib/python3.7/site-packages/concoct-1.0.0-py3.7-linux-x86_64.egg/EGG-INFO/scripts/concoct", line 88, in results = main(args) File "/home/naima17/virtual_env/Concoct/lib/python3.7/site-packages/concoct-1.0.0-py3.7-linux-x86_64.egg/EGG-INFO/scripts/concoct", line 20, in main composition, cov, cov_range = load_data(args) File "/home/naima17/virtual_env/Concoct/lib/python3.7/site-packages/concoct-1.0.0-py3.7-linux-x86_64.egg/concoct/input.py", line 25, in load_data read_length = args.read_length File "/home/naima17/virtual_env/Concoct/lib/python3.7/site-packages/concoct-1.0.0-py3.7-linux-x86_64.egg/concoct/input.py", line 90, in load_coverage cov.ix[:,cov_range[0]:cov_range[1]] = cov.ix[:,cov_range[0]:cov_range[1]].add( File "/home/naima17/virtual_env/Concoct/lib/python3.7/site-packages/pandas/core/generic.py", line 5274, in getattr return object.getattribute(self, name) AttributeError: 'DataFrame' object has no attribute 'ix'

May be it's a python version issue? Thanks in advance Naima

Marlinski95 commented 1 year ago

Hi! I am having the same issue! Has there been a solution to this? It seems like it is index data frame issue in the pandas methods in the script based on my readings. However, I am not sure if that is something we as enduser can/should try to fix. Could anybody assist with this? @alneberg? Any help would be greatly appreciated!