Closed ChrisCarrie closed 5 years ago
BaselAbujamous
commented
5 years ago Hi Chris
Thanks for using Clust and for your question.
It seems that you have installed Clust using python 3 (pip3), and unfortunately Clust is not compatible with it, and causes such errors (and other errors). I suggest uninstalling clust, and reinstalling it using Python 2 (using pip install clust).
I hope this solves your problem. Please let me know if it is still unsolved after this.
All the best. Basel
ChrisCarrie
commented
5 years ago Hi Basel
Yep that fixedit. Is running fine on single inputs.
I am trying to run it over 2 species with basically the same time points. I have run orthologs for these to create the mapping ID files. However I keep getting this issue
| Analysis started at: Monday 21 January 2019 (16:44:19) |
| 1. Reading dataset(s) |
| 2. Data pre-processing |
Traceback (most recent call last):
File "/home/chris/.local/bin/clust", line 11, in
I have tried just about everything I can think of. Not entirely sure what the issue is. Any ideas?
Cheers Chris
BaselAbujamous
commented
5 years ago Hi Chris
Thanks again for your interest and for reporting this. This is the same issue #28, which has been fixed now in version 1.8.11.
All the best, Basel
BaselAbujamous
commented
5 years ago Hi Chris,
Update: Clust 1.10.0 now is compatible with Python 3 (as well as 2.7)!
All the best
Hi Basel
I keep getting this error any ideas how to fix it.
chris@chris-ubuntu:~$ clust /media/chris/E27C21847C215497/Clust/clust-1.8.10/X1.txt
/===========================================================================\ | Clust | | (Optimised consensus clustering of multiple heterogenous datasets) | | Python package version 1.8.10 (2018) Basel Abu-Jamous | +---------------------------------------------------------------------------+ | Analysis started at: Monday 21 January 2019 (12:30:51) | | 1. Reading dataset(s) | Traceback (most recent call last): File "/home/chris/anaconda3/bin/clust", line 11, in
sys.exit(main())
File "/home/chris/anaconda3/lib/python3.6/site-packages/clust/main.py", line 98, in main
args.cs, args.np, args.optimisation, args.q3s, args.basemethods, args.deterministic)
File "/home/chris/anaconda3/lib/python3.6/site-packages/clust/clustpipeline.py", line 84, in clustpipeline
returnSkipped=True)
File "/home/chris/anaconda3/lib/python3.6/site-packages/clust/scripts/io.py", line 46, in readDatasetsFromDirectory
datafilesread = readDataFromFiles(datafileswithpath, delimiter, float, skiprows, skipcolumns, returnSkipped)
File "/home/chris/anaconda3/lib/python3.6/site-packages/clust/scripts/io.py", line 193, in readDataFromFiles
usecols=range(skipcolumns, ncols), na_filter=True, comments=comm)
File "/home/chris/anaconda3/lib/python3.6/site-packages/clust/scripts/io.py", line 227, in pdreadcsv_regexdelim
result = pd.read_csv(StringIO('\n'.join(re.sub(delimiter, b'\t', x) for x in f)),
File "/home/chris/anaconda3/lib/python3.6/site-packages/clust/scripts/io.py", line 227, in
result = pd.read_csv(StringIO('\n'.join(re.sub(delimiter, b'\t', x) for x in f)),
File "/home/chris/anaconda3/lib/python3.6/re.py", line 191, in sub
return _compile(pattern, flags).sub(repl, string, count)
TypeError: sequence item 1: expected str instance, bytes found
Hope that makes sense Cheers