problem with get_scores #9
Description
it seems that pharmd installs psearch from the masters branch. so, when I did the get_scores, it said that
"no module named psearch.database".
I tried to play around, and found that the psearch@gen_pharms branch has a database.py file which is not present in the masters branch, I took it and placed it in the psearch folder installed when installing Pharma.
However, the following message appears when trying to get scores using cca approach
return mod.open(file, flag, mode)
_dbm.error: [Errno 79] Inappropriate file type or format: 'compounds'
P.S. compounds is the name of the db file generated from prepare_db.py
and when I tried CHA approach,
File "parsers.pyx", line 838, in pandas._libs.parsers.TextReader.read_low_memory
File "parsers.pyx", line 921, in pandas._libs.parsers.TextReader._read_rows
File "parsers.pyx", line 983, in pandas._libs.parsers.TextReader._convert_column_data
pandas.errors.ParserError: Too many columns specified: expected 3 and found 2