search

compomics / moFF

A modest Feature Finder (moFF) to extract MS1 intensities from Thermo raw file
Apache License 2.0
33 stars 11 forks source link

apex terminated: pandas.parser is deprecated #18

Closed lcscs12345 closed 7 years ago

lcscs12345 commented 7 years ago

Hi,

Thank you for your platform independent CLI tool. I received the following error when running this command:

$ python ~/proteomics/src/moFF-1.0/moff.py --tol "10" --inputtsv "test/psm.tsv" --inputraw "test/example.RAW" --output_folder "out"

.../moFF-1.0/moff.py:288: FutureWarning: pandas.parser is deprecated and will be removed in a future version. You can access CParserError as pandas.errors.ParserError except pd.parser.CParserError:

Here are the versions of the dependencies: pandas: 0.20.3-py27_0 numpy: 1.13.1-py27_0
argparse: 1.4.0-py27_0 scikit-learn: 0.19.0-np113py27_0 pymzml: 0.7.8

Maux82 commented 7 years ago

Hi,

but does it stop moFF ? or it is just a warning ? I will do some test on Pandas 20.3, to see what it is the problem and I will let you know.

Are sure that the input file is a valid tab-delimited file ?

lcscs12345 commented 7 years ago

I ran more tests and found out that moFF works on the same tsv and RAW files only when they are located in the moFF subdirectory such as sample_data. This error has nothing to do with the version of dependencies.

The following example won't work: $ pwd /root/src/moFF/ $ ls /root/src/moFF/sample_data/test 20080315_CPTAC6_07_6A005.RAW 20080315_CPTAC6_07_6A005.txt $ cd /root/src/moFF/sample_data $ python ~/src/moFF/moff.py --tol "10" --inputtsv "test/20080315_CPTAC6_07_6A005.txt" --inputraw "test/20080315_CPTAC6_07_6A005.RAW"

Maux82 commented 7 years ago

yes, the input file path of the should be a relative from the path where the moFF folder is located.

Maybe I can try to fix it to make it more general. I thought that it was not a big missing but of couse it is also it is not mentioned in the documentation.