1 How to use TraceGroomer

How to use TraceGroomer in the command line

The execution of TraceGroomer takes only few seconds. Below we explain how to proceed.

Please prepare your files as explained the section 2 Input files.

Once your input files are ready, and that you have the following structure, you must organize your files as follows:

MyProject
├── data
│   ├── dataset1_data
│   │   ├── metadata_1.csv
│   │   └── TRACER_IsoCor_out_example.tsv
└── groom_files
    └── dataset1
          ├── amount_material_weightorcells.csv
          └── config-1-groom.yml

This structure is recommended to easily re-use the data folder for DIMet.

The command is:

python3 -m tracegroomer --targetedMetabo_path $MEASUREMENTS \
    --type_of_file $MY_TYPE_OF_INPUT \
    $MY_BASIC_CONFIG

Where :

• MEASUREMENTS is the file that contains the measurements, in absolute path.
• MY_TYPE_OF_INPUT corresponds to one of: IsoCor_out_tsv, VIBMEC_xlsx, generic_xlsx

We recommend to run a test with the provided examples if this is the first time you use TraceGroomer. Then re-use the organization and the configuration as template, and modify the command to be suitable to your data.

Running a test with the provided examples

To perform a test using the examples we provide, please download and uncompress our examples from Zenodo. The structure of the folder is:

examples_TraceGroomer
├── data
│   ├── example-isocor_data
│   │   ├── metadata_1.csv
│   │   └── TRACER_IsoCor_out_example.tsv
│   ├── example-sheet_data
│   │   ├── metadata_3.csv
│   │   └── TRACER_generic_sheet.xlsx
│   └── example-vib_data
│       ├── metadata_2.csv
│       └── TRACER_metabo_2.xlsx
└── groom_files
    ├── example-isocor
    │   ├── amount_material_weightorcells.csv
    │   └── config-1-groom.yml
    ├── example-sheet
    │   └── config-3-groom.yml
    └── example-vib
        ├── config-2-groom.yml
        ├── nbcells-or-amountOfMaterial.csv
        └── reject_list.csv

These examples correspond to:

1. example-isocor_data: IsoCor data (tsv file)
2. example-vib_data: VIB MEC xlsx file
3. example-sheet_data: "generic" type of xlsx file

Run the script

Note : if the working folder is not the 'home' directory, modify accordingly the absolute paths in the .yml files and in the bash commands.

For IsoCor data:

python3 -m tracegroomer \
   --targetedMetabo_path ~/examples_TraceGroomer/data/example-isocor_data/TRACER_IsoCor_out_example.tsv \
   --type_of_file IsoCor_out_tsv \
   ~/examples_TraceGroomer/groom_files/example-isocor/config-1-groom.yml

or, for VIB MEC data:

python3 -m tracegroomer \
  --targetedMetabo_path ~/examples_TraceGroomer/data/example-vib_data/TRACER_metabo_2.xlsx \
  --type_of_file VIBMEC_xlsx 
  ~/examples_TraceGroomer/groom_files/example-vib/config-2-groom.yml

or, for the generic case:

python3 -m tracegroomer --targetedMetabo_path ~/examples_TraceGroomer/data/example-sheet_data/TRACER_generic_sheet.xlsx \
   --type_of_file generic_xlsx 
   ~/examples_TraceGroomer/groom_files/example-sheet/config-3-groom.yml

The output

Thet files are saved in the folder that you specified in the config .yml file (groom_out_path field). The data/[my_dataset] location is recommended for saving the output. A total of 4 output files are generated if the absolute isotopologues are provided, otherwise 3 files are generated.

In this way you simply copy the entire data/ content to the folder structure that we want to run with DIMet !

The format of these output files is tab-delimited .csv.