twbattaglia / koeken Goto Github PK

Hello,

I have been trying to create cladogram with plot_caldogram.py function but every time I run that command I'm getting an error saying that input-output files are not recognized. What should be the input file to run this function?

thank you

I'm trying to run your script but I get an error. I assume it has something to do with my mapping file but I am not sure how I need to fix it.

Also I don't really have time points in my data. All I want to see is there a differential abundance of OTUs between sites. My group significance data from QIIME suggest there is but I'd like to see this visualized in Lefse. Please help!!! Thanks.

/macqiime/anaconda/lib/python2.7/site-packages/rpy2/rinterface/init.py:186: RRuntimeWarning: Error in kruskal.test.default(c(0, 25.0400641025915, 0, 0, 0, 0, 0, 0, :
all observations are in the same group

warnings.warn(x, RRuntimeWarning)
Traceback (most recent call last):
File "/macqiime/anaconda/bin/run_lefse.py", line 67, in
kw_ok,pv = test_kw_r(cls,feat_values,params['anova_alpha'],sorted(cls.keys()))
File "/macqiime/anaconda/bin/lefse.py", line 59, in test_kw_r
kw_res = robjects.r('kruskal.test('+fo+',)$p.value')
File "/macqiime/anaconda/lib/python2.7/site-packages/rpy2/robjects/init.py", line 362, in call
res = self.eval(p)
File "/macqiime/anaconda/lib/python2.7/site-packages/rpy2/robjects/functions.py", line 178, in call
return super(SignatureTranslatedFunction, self).call(*args, **kwargs)
File "/macqiime/anaconda/lib/python2.7/site-packages/rpy2/robjects/functions.py", line 106, in call
res = super(Function, self).call(*new_args, **new_kwargs)
rpy2.rinterface.RRuntimeError: Error in kruskal.test.default(c(0, 25.0400641025915, 0, 0, 0, 0, 0, 0, :
all observations are in the same group

Traceback (most recent call last):
File "/macqiime/anaconda/bin/plot_cladogram.py", line 345, in
clad_tree = read_data(params['input_file'],params)
File "/macqiime/anaconda/bin/plot_cladogram.py", line 105, in read_data
with open(input_file, 'r') as inp:
IOError: [Errno 2] No such file or directory: 'test//lefse_output/run_lefse/Third.txt'
map_gut_final6.txt

Hello,

I have been using the koeken.py script for a very long time and I must confess that this script helped me a lot with my analysis. I have been using this script in a virtual environment the whole this time since my OS is windows and it has worked very well in a virtual box. However, it has become difficult to run virtual box parallel with other works. In addition, this script is based on python <3 version making it impossible to install in windows (I have tried many ways- via ubuntu, installing python <3, etc). So I would like to know if it is possible to work around the virtual environment to run this script? Most likely implementation of this script in python >3 versions. I would really appreciate your help and time. Thank you.