iamredrum/ltm

Latent tree models for phylogenetic inference of single-cell data

Running LTM Pipeline

The pipeline runs the latent tree model (LTM) algorithm on a copy number matrix to generate a tree.

Installation:

conda install --file conda_packages.txt
python setup.py install

The LTM pipeline also requires the installation of pypeliner and pypeliner utils:

git clone https://bitbucket.org/dranew/pypeliner.git
cd pypeliner
python setup.py install

git clone https://svn.bcgsc.ca/bitbucket/scm/pp/pypeliner_utils.git
cd pypeliner_utils
python setup.py install

Preprocessing the data:

The LTM pipeline is usually run with data generated from multiple runs of the single cell pipeline. The outputs of the single cell pipeline need to be processed before it can be used as input for the LTM pipeline. This is done by running generate_ltm_inputs.py as follows:

python generate_ltm_inputs.py SA535.csv SA535

In the example above, SA535.csv is a .csv file of all single cell analysis objects that make up the tree for the given sample ID and SA535 is the sample ID of the tree. For example, SA535.csv would contain the following:

jira_ticket,library_id,analysis_ploidy
SC-893,A96165B,autoploidy
SC-787,A95732A,autoploidy
SC-856,A95736A,autoploidy

• jira_ticket is the Jira ticket number of each constituent single cell analysis
• library_id is the DLP library ID associated with the single cell analysis
• analysis_ploidy is the ploidy of the single cell analysis to be used in the tree

Optionally, the flag --output_dir can be used to specify the output directory for the sample. The default value is ./output/.

The script looks for a copy number matrix in /genesis/shahlab/danlai/SC-803/hmmcopy/merged_output/<jira_ticket>/<analysis_ploidy>/<library_id>_cn_matrix.csv and a metrics summary file in /genesis/shahlab/danlai/SC-803/hmmcopy/merged_output/<jira_ticket>/<analysis_ploidy>/<library_id>_all_metrics_summary.csv. If a copy number matrix does not exist for the Jira ticket, the script will generate one. To do this, it looks for the files /projects/sftp/shahlab/singlecell/<jira_ticket>/hmmcopy_<analysis_ploidy>/<library_id>_hmmcopy.h5 and /projects/sftp/shahlab/singlecell/<jira_ticket>/alignment/<library_id>_alignment_metrics.h5. It then uses a classifier to generate the file <output_dir>/<jira_ticket>_all_metrics_summary_classified.csv.

The script must be run from a location that can see the single cell pipeline results in SFTP (/projects/sftp/)

The metrics summary file is the used to filter for cells with quality >= 0.75. The copy number matrices are then merged and filtered for bins with mappability >= 0.99. The resulting copy number matrix is then written to a .csv file in the output directory.

Running the LTM pipeline:

ltm ltm/test_data/cn_matrix.csv output/ltm/

The first argument is the path to the copy number matrix file that was generated during preprocessing, and the second is the path to the output directory.

Optional arguments are:

• --root_id: ID of the cell to be used as the root of the tree. Default: the first SA928 cell
• --config_file: path to the configuration file to be used for the pipeline. Default: config/ltm.yaml
• --filtered_cells: text file of cells to analyze. Default: all cells are analyzed
• --ltm_method: method used for learning (CLG or RG). Default: CLG
• --scale: use the scaled minimum spanning tree method. Default: false
• --number_of_jobs: if the scaled method is used, the number of jobs to submit to the cluster. Default: 10

To run the pipeline locally,

ltm ltm/test_data/cn_matrix.csv output/ltm/ --loglevel DEBUG --submit local

To submit the pipeline to the job queue,

ltm ltm/test_data/cn_matrix.csv output/ltm/ --loglevel DEBUG --submit asyncqsub --nativespec ' -hard -q shahlab.q -P shahlab_high -V -l h_vmem={mem}G -pe ncpus {ncpus}'