CLI
A command line interface (CLI) is available in Trisicell package.
After you have trisicell correctly installed on your machine
(see installation tutorial), the trisicell
command will become available in the terminal. trisicell is a
command line tool with subcomands. You can get quick info on all the
available commands typing trisicell --help. You will get the
following output:
Usage: trisicell [OPTIONS] COMMAND [ARGS]...
Trisicell.
Scalable intratumor heterogeneity inference and validation from single-cell data.
Options:
--version Show the version and exit.
--help Show this message and exit.
Commands:
mcalling Mutation calling.
booster Boost available tree reconstruction tool (Trisicell-Boost).
partf Get samples or calculate for PartF.
consensus Build consensus tree between two phylogenetic trees (Trisicell-Cons).
mcalling - Run Mutation Calling
trisicell
Trisicell.
Scalable intratumor heterogeneity inference and validation from single-cell data.
trisicell [OPTIONS] COMMAND [ARGS]...
Options
- --version
Show the version and exit.
mcalling
Mutation calling pipeline.
trisicell mcalling config.yml
A template of the config file can be found here.
trisicell mcalling [OPTIONS] CONFIG_FILE
Options
- -t, --test
Is in test mode.
- Default
False
- -s, --status
Check the status of runs.
- Default
False
- -b, --build
Build the final matrices of genotype and expression.
- Default
False
- -c, --clean
Cleaning the directory including removing intermediate files.
- Default
False
Arguments
- CONFIG_FILE
Required argument
booster - Run Booster
trisicell
Trisicell.
Scalable intratumor heterogeneity inference and validation from single-cell data.
trisicell [OPTIONS] COMMAND [ARGS]...
Options
- --version
Show the version and exit.
booster
Boost available tree reconstruction tool.
For doing all 3 steps:
trisicell booster input.SC 0.001 0.1 –solver scite –n_samples 200 –sample_size 15 –n_jobs 4 –n_iterations 10000 –dep_weight 50 –subsample_dir . –begin_index 0
For doing only the last step:
trisicell booster input.SC 0.001 0.1 –dep_weight 50 –subsample_dir PATH_TO_SUBSAMPLES_FOLDER –no_subsampling –no_dependencies
trisicell booster [OPTIONS] GENOTYPE_FILE ALPHA BETA
Options
- --solver <solver>
Solver of the booster.
- Default
scite- Options
scite | phiscs | scistree
- --sample_on <sample_on>
Sampling on
mutsorcells.- Default
muts- Options
muts | cells
- --sample_size <sample_size>
The size of samples i.e. the number of muts or cells.
- Default
10
- --n_samples <n_samples>
The number of subsamples.
- Default
10
- --begin_index <begin_index>
ID of the start subsample name.
- Default
0
- --n_jobs <n_jobs>
Number of parallel jobs to do subsampleing.
- Default
0
- --dep_weight <dep_weight>
Weight for how many subsamples to be used in dependencies calculation.
- Default
50
- --time_limit <time_limit>
Timeout of solving allowance (in second).
- Default
120
- --n_iterations <n_iterations>
SCITE number of iterations.
- Default
500000
- --subsample_dir <subsample_dir>
A path to the subsamples directory.
- --disable_tqdm
Disable showing the tqdm progress.
- Default
False
- --no_subsampling
No running of subsampling (step 1/3).
- Default
False
- --no_dependencies
No running of subsampling (step 2/3).
- Default
False
- --no_reconstruction
No running of reconstruction (step 3/3).
- Default
False
Arguments
- GENOTYPE_FILE
Required argument
- ALPHA
Required argument
- BETA
Required argument
consensus - Run Consensus
trisicell
Trisicell.
Scalable intratumor heterogeneity inference and validation from single-cell data.
trisicell [OPTIONS] COMMAND [ARGS]...
Options
- --version
Show the version and exit.
consensus
Build consensus tree between two phylogenetic trees.
It writes the conflict-free matrix representing the consensus tree
into the consensus_path filepath.
trisicell consensus first_tree.CFMatrix second_tree.CFMatrix
trisicell consensus [OPTIONS] FIRST_TREE SECOND_TREE CONSENSUS_PATH
Arguments
- FIRST_TREE
Required argument
- SECOND_TREE
Required argument
- CONSENSUS_PATH
Required argument