Lewis Research Group (LRG) codebase for omics data generation, processing, quality control and integration.
git clone [email protected]:LewisResearchGroup/lrg-omics.git
cd lrg-omics
conda env create -f dev/conda/environment.yml
conda activate lrg
pip install -e .
conda activate lrg
python -m ipykernel install --name lrg --display-name 'LRG' --user
- Soren Wacker
- Mario Ernesto-Valdés
- Luis Ponce Alvares
- Estefania Barreto-Ojeda (@ojeda-e)
- Support for Python 3.6 and 3.7 was dropped.
A script to run MaxQuant runs from the Linux command line. The script can be used to on SLURM HPC clusters to create and submit jobs. The job is executed in the temporary directory --run-dir and then the only the results are copied to the output directory --out-dir. By default a unique id is added to the rundir name and the run is executed in a subdirectory of --run-dir which is the name of the .RAW file that is going to be processed. This way many files can be processed with the same settings without confusing the results. One limitation of the script is that it expects exactly one .RAW file per run. It is not tested for multiple .RAW files at once. If you have installed MaxQuant with conda, the you can use --maxquantcmd maxquant. You can run any version of MaxQuant using mono. In that case the command loosk like --maxquantcmd "mono /path/to/MaxQuantCmd.exe". Note that, not every monoversion works with everyMaxQuant` version.
usage: lrg_run_maxquant.py [-h] --raw [RAW ...] --fasta FASTA --mqpar MQPAR [--run-dir RUN_DIR] [--out-dir OUT_DIR] [--cold-run] [--rerun] [--submit] [--batch-cmd BATCH_CMD] --maxquantcmd MAXQUANTCMD [--add-raw-name-to-outdir]
[--add-uuid-to-rundir] [--cleanup] [--verbose]
Process MaxQuant runs.
options:
-h, --help show this help message and exit
--raw [RAW ...] RAW files to process.
--fasta FASTA Fasta file.
--mqpar MQPAR MaxQuant parameter template file (mqpar.xml).
--run-dir RUN_DIR Temporary directory to perform the calculation.
--out-dir OUT_DIR Location of the final results.
--cold-run Just simulate run and show the actions.
--rerun Start the run even if results already exist.
--submit Submit slurm job.
--batch-cmd BATCH_CMD
Additional commands for slum job script e.g. "source .bashrc conda activate omics;...".
--maxquantcmd MAXQUANTCMD
Command to start MaxQuant e.g. "mono MaxQuantCmd.exe".
--add-raw-name-to-outdir
Do not add subdirectory raw file name to run directory.
--add-uuid-to-rundir Do not add uuid to run directory.
--cleanup Remove run directory after running MaxQuant
--verbose
A script that can be used to convert metabolomics mzML files to mzMLb format. The script uses the psims library.
usage: lrg_mzML2mzMLb.py [-h] [-i INPUT] [-o OUTPUT] [-d OUTPUT_DIRECTORY]
options:
-h, --help show this help message and exit
-i INPUT, --input INPUT
-o OUTPUT, --output OUTPUT
-d OUTPUT_DIRECTORY, --output-directory OUTPUT_DIRECTORY
Command line tool to extract data from ThermoFisher instrument worklists.
Usage: cat [OPTION]... [FILE]...
Concatenate FILE(s) to standard output.
With no FILE, or when FILE is -, read standard input.
-A, --show-all equivalent to -vET
-b, --number-nonblank number nonempty output lines, overrides -n
-e equivalent to -vE
-E, --show-ends display $ at end of each line
-n, --number number all output lines
-s, --squeeze-blank suppress repeated empty output lines
-t equivalent to -vT
-T, --show-tabs display TAB characters as ^I
-u (ignored)
-v, --show-nonprinting use ^ and M- notation, except for LFD and TAB
--help display this help and exit
--version output version information and exit
Examples:
cat f - g Output f's contents, then standard input, then g's contents.
cat Copy standard input to standard output.
from lrg_omics.metabolomics.Eatogram import Eatogram
eatogram = Eatogram('input/230420-MINT__LSARP-FAES__results.csv', # MINT results table
'input/230420-MINT__LSARP-FAES__metadata.csv', # MINT metadata table
'E. faecium')
eatogram.run()
plt.title('$E. faecium$')
