Parse data from Pion Sirius T3 instrument XML files
First clone and install the repo
git clone [email protected]:OpenADMET/t3-chomper.git
cd t3-chomper
pip install -e . Or download and install a whl file from a release
pip install t3_chomper-0.1.5-py3-none-any.whl One can then parse file(s) from the T3 instrument using the CLI. One can parse from one file or a directory of t3r result files. The user must specify whether you are parsing pka data or logp data with the --protocol argument. Parsed results will be written to a csv file.
# Extract pka data from a file named my_data.t3r to pka_output.csv
t3_extract my_data.t3r --protocol pka --output pka_output.csv
# Extract logp data from a directory /home/data/logp_files to logp_output.csv
t3_extract /home/data/logp_files/ --protocol logp --output logp_output.csv
# Extract pka data from a file and write to stdout
t3_extract my_data.t3r --protocol pka One can also generate CSV import files for creating experiments. For this, one needs a registration file with sample information and a pKa data file with estimated pKas. There are several defined experimental tray layouts which can be listed by viewing the help dialog:
t3_gencsv --helpThe registration file should have the following columns:
| Column | Description |
|---|---|
| ID | compound ID (must match pKa data file) |
| Registry Number | compound name in registry |
| Batch Name | Name/number of compound batch |
| Well | well in plate |
| MW | molecular weight |
| FW | formula weight |
| mg | mass in mg |
The pKa data file can be in one of two formats:
The short format includes one row for each compound and one column for all pKas per compound. It uses the same comma-separated format that the T3 instrument uses.
| Column | Description |
|---|---|
| vendor_id | compound ID (must match registration file) |
| reformatted_pkas | comma-separated list of pKas and types in ascending order: e.g. "ACID,2.5,BASE,9.3" |
The long format includes one row for each pKa. Compounds with multiple pKas will appear in multiple rows.
| Column | Description |
|---|---|
| vendor_id | compound ID (must match registration file) |
| pka_value | value of pka |
| pka_type | type of pka ("acid" or "base") |
| TrayFormat | Description |
|---|---|
| fastuvpska | 47 samples per tray, with one calibration |
| phmetric | 24 samples per tray, with 1x cleanup step after each |
| uvmetric | 24 samples per tray, calibration before each sample |
| logp | 16 samples per tray, with 2x cleanup steps after each |
Files for each tray will be generated in the output directory provided with the --output argument.
# Generate csv experiment import files with fastuvpska format
t3_gencsv --regi <registration file> --pka <pKa data file> --protocol fastuvpska --output <new_pka_experiment_dir>
# Generate csv experiment import files with logp format
t3_gencsv --regi <registration file> --pka <pKa data file> --protocol logp --output <new_logp_experiment_dir>