search

BaselAbujamous / clust

Automatic and optimised consensus clustering of one or more heterogeneous datasets
Other
160 stars 35 forks source link

TypeError: Cannot cast array from dtype('O') to dtype('float64') according to the rule 'safe' #49

Closed maxnest closed 4 years ago

maxnest commented 4 years ago

First of all thanks for this great and useful tool! Unfortunately, I encountered the following error:

/===========================================================================\ | Clust | | (Optimised consensus clustering of multiple heterogenous datasets) | | Python package version 1.10.8 (2019) Basel Abu-Jamous | +---------------------------------------------------------------------------+ | Analysis started at: Friday 01 November 2019 (00:46:42) | | 1. Reading dataset(s) | Traceback (most recent call last): File "pandas/_libs/parsers.pyx", line 1191, in pandas._libs.parsers.TextReader._convert_tokens TypeError: Cannot cast array from dtype('O') to dtype('float64') according to the rule 'safe'

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/home/maxnestlcl/anaconda3/bin/clust", line 12, in sys.exit(main()) File "/home/maxnestlcl/anaconda3/lib/python3.7/site-packages/clust/main.py", line 103, in main args.cs, args.np, args.optimisation, args.q3s, args.basemethods, args.deterministic) File "/home/maxnestlcl/anaconda3/lib/python3.7/site-packages/clust/clustpipeline.py", line 86, in clustpipeline returnSkipped=True) File "/home/maxnestlcl/anaconda3/lib/python3.7/site-packages/clust/scripts/io.py", line 46, in readDatasetsFromDirectory datafilesread = readDataFromFiles(datafileswithpath, delimiter, float, skiprows, skipcolumns, returnSkipped) File "/home/maxnestlcl/anaconda3/lib/python3.7/site-packages/clust/scripts/io.py", line 205, in readDataFromFiles usecols=range(skipcolumns, ncols), na_filter=data_na_filter, comments=comm) File "/home/maxnestlcl/anaconda3/lib/python3.7/site-packages/clust/scripts/io.py", line 240, in pdreadcsv_regexdelim delimiter='\t', dtype=dtype, header=None, skiprows=skiprows, usecols=usecols, na_filter=na_filter, comment=comments).values File "/home/maxnestlcl/anaconda3/lib/python3.7/site-packages/pandas/io/parsers.py", line 702, in parser_f return _read(filepath_or_buffer, kwds) File "/home/maxnestlcl/anaconda3/lib/python3.7/site-packages/pandas/io/parsers.py", line 435, in _read data = parser.read(nrows) File "/home/maxnestlcl/anaconda3/lib/python3.7/site-packages/pandas/io/parsers.py", line 1139, in read ret = self._engine.read(nrows) File "/home/maxnestlcl/anaconda3/lib/python3.7/site-packages/pandas/io/parsers.py", line 1995, in read data = self._reader.read(nrows) File "pandas/_libs/parsers.pyx", line 899, in pandas._libs.parsers.TextReader.read File "pandas/_libs/parsers.pyx", line 914, in pandas._libs.parsers.TextReader._read_low_memory File "pandas/_libs/parsers.pyx", line 991, in pandas._libs.parsers.TextReader._read_rows File "pandas/_libs/parsers.pyx", line 1123, in pandas._libs.parsers.TextReader._convert_column_data File "pandas/_libs/parsers.pyx", line 1197, in pandas._libs.parsers.TextReader._convert_tokens ValueError: could not convert string to float: 'TPA_4h'

Thanks!

maxnest commented 4 years ago

Dear authors and colleagues, Solution for this problem is quite simple: directory with data must not to contain other files, including the description of the design of the experiment (like in my case: ValueError: could not convert string to float: 'TPA_4h'). Once again thanks you for a great program!

BaselAbujamous commented 4 years ago

@maxnest Thanks for using clust, and happy to see the issue resolved.

I hope you get the results you like from the method and best of luck in your research. Please let me know if other problems appear.

Basel