Command Line Interface (CLI)

The command-line interface can be used by calling the CoMPaseD_CLI.py command.

All parameters required for the different steps of CoMPaseD can be set in the parameters file provided in the GitHub repository.

Note

Many of these parameters can be directly overwritten through the command-line arguments.

A full list of command-line arguments with explanations can be displayed using the -h flag.

python CoMPaseD_cli.py -h

Options

Parameter Type	Command Line Argument	Description
Help	-h, –help	show the help message and exit
Parameter File	-p, –param_file	path to CoMPaseD parameter file
CoMPaseD Mode	-e, –export	export simulated protein abundance values
CoMPaseD Mode	-d, –digest	perform in-silico digest using crux toolkit
CoMPaseD Mode	-a, –analysis	perform analysis from simulated protein abundance and in-silico digestion
Digestion Mode Arguments	–use_original_proteomapper	use original perl scripts for mapping in-silico digested peptides, this might be slower but requires less memory
Digestion Mode Arguments	–differentiate_I_L	distinguish between peptide variants containing leucine or iso-leucine (default treat as identical)
Digestion Mode Arguments	–indexing_key_len	length in amino acids of the indexing keys for mapping
Analysis Mode Arguments	–export_result	path to CoMPaseD export result file with simulated protein abundance values and protein group assignment
Analysis Mode Arguments	–digestion_result	path to CoMPaseD digestion result file (‘unique_peptides_table_filtered’)
Overwrite Parameter File	–out_folder	change output directory
Overwrite Parameter File	–fasta	change fasta file
Overwrite Parameter File	–score_peptide	change weight of peptide IDs for protease score calculation
Overwrite Parameter File	–score_protein	change weight of protein IDs for protease score calculation
Overwrite Parameter File	–score_coverage	change weight of protein coverage for protease score calculation
Overwrite Parameter File	–enzymes	change enzymes
Overwrite Parameter File	–mc	change maximal missed cleavage sites
Overwrite Parameter File	–mc_freq	change missed cleavage sites frequency
Overwrite Parameter File	–num_peps	change number of peptides to sample
Overwrite Parameter File	–min_pep_mw	minimal molecular weight of peptides after digestion in Da (default: 400)
Overwrite Parameter File	–max_pep_mw	maximal molecular weight of peptides after digestion in Da (default: 6000)
Overwrite Parameter File	–min_pep_len	minimal length of peptides after digestion in amino acids (default: 6)
Overwrite Parameter File	–max_pep_len	maximal length of peptides after digestion in amino acids (default: 55)
Overwrite Parameter File	–frac_peps	change fraction of generated peptides to sample
Overwrite Parameter File	–bins	change protein binning
Overwrite Parameter File	–undetectable	change undetectable protein fraction in protein bins
Overwrite Parameter File	–DMSP_weight	change weighting factor of Deep-MS-Peptide prediction
Overwrite Parameter File	–DMSP_model	change Deep-MS-Peptide prediction model path
Overwrite Parameter File	–samplings	change number of random samplings
Overwrite Parameter File	–dynamic_range	change dynamic range of protein abundance
Overwrite Parameter File	–use_unique_peptides_only	change whether to use only unique peptides or assemble protein groups and consider shared peptides (default is true)

To run the full analysis provided by CoMPaseD use the following command.

python CoMPaseD_cli.py -p path/to/parameters

To run specific parts of the analysis, the export (-e), digestion (-d) or result analysis (-a) flags can be used.

python CoMPaseD_cli.py -p path/to/parameter.param [-e] [-d] [-a]

Note

The [-a] flag requires to run the rest of the analysis beforehand [-e] and [-d].

All result files are written to the folder/files indicated in the parameters file or given as command-line arguments.

Advanced usage

For complex analyses or the comparison of different settings, CoMPaseD can be used in a command line mode by executing CoMPaseD_CLI.py. This also allows the automation of several analyses via shell scripts or batch files.

For example, the following commands in a Windows batch file would run an analysis with identical parameters for three different organisms and output the results to folders named Organism_1, Organism_2 and Organism_3:

CoMPaseD_cli.py -p C:\CoMPaseD.param --out_folder C:\Result\Organism_1 --fasta C:\Organism_1.fasta

CoMPaseD_cli.py -p C:\CoMPaseD.param --out_folder C:\Result\Organism_2 --fasta C:\Organism_2.fasta

CoMPaseD_cli.py -p C:\CoMPaseD.param --out_folder C:\Result\Organism_3 --fasta C:\Organism_3.fasta

Similarly, the following command in a Linux shell script would run one analysis with each of the two Deep MS-Peptide models using an existing export and digestion file which was specified in the parameter file:

python3 /home/user/CoMPaseD/CoMPaseD_cli.py -p /home/user/CoMPaseD.param -a --DMSP_model /home/user/CoMPaseD/bin/DeepMSPep_Confetti_Model.h5 --out_folder /home/user/results/confetti_model/

python3 /home/user/CoMPaseD/CoMPaseD_cli.py -p /home/user/CoMPaseD.param -a --DMSP_model /home/user/CoMPaseD/bin/DeepMSPep_Original_Model.h5 --out_folder /home/user/results/original_model/

Command line options will generally overwrite values in the parameter file, and a parameter file with the used values will automatically be saved in the output folder together with the results. The complete list of options available can be displayed by executing:

CoMPaseD_cli.py --help