Sapling

Sapling is a method that infers a small set of backbone trees on a smaller subset of mutations that collectively summarize the entire set of possible phylogenies. Sapling can also grow a given backbone tree into a full phylogeny.

Dependencies

Sapling requires the following python packages:

• numpy
• cvxopt/gurobipy (at least one, using cvxopt by default, progressive LP (-L pLP) is faster but requires gurobipy)

I/O Format

Sapling takes a TSV(tab-separated values) file as input. The first line includes the names of the columns, the following colunms are required:

• sample_index (0, 1, ..., m-1) for m samples
• mutation_index (0, 1, ..., n-1) for n mutations
• var variant reads
• depth total reads
• cluster_index(optional) (0, 1, ..., k-1) for k clusters

Here is an example of input.

The output is a text file. The first line includes the the number backbone trees, in the format of "# $\tau$ backbone trees". Depending on the size $\ell$ of the set of mutations covered in the backbone trees, for the following $\tau \times \ell$ lines, each $\ell$ lines conatins a a tree. More specifically, the first line of the $\ell$ lines includes the number mutations (mutation clusters) included in the backbone tree, and the following $\ell$-1 lines are descriptions of the edges of the tree in the format of "v1 v2" indicating that v1 is the unique parent of v2 in this tree. (-1 means germline)

Usage instructions

Infer backbone trees (main program)

Usage:
  python main.py [-h] -f str -o str -a float [-l int] [-t int] [-m] [-L str]
Where:
  -h
     Print a short help message
  -f str
     Input file
  -o str
     output file
  -a float
     rho: lower bound factor of likelihood
  -l int
     ell: size of the mutation set, will overide -t if provide any (default: None)
  -t int
     tau: upperbound of the number of backbone trees (default: 5)
  -m
     allow multiple evolutions from germline (GL)
  -L str:
     method to solve LLH: cvxopt/pLP (default: cvxopt)

Example command: python main.py -f example.tsv -o example.txt -a 0.9

The output of the above command on the example input.

Expand backbone trees into full trees (greedy expand)

Usage:
    python greedy_expand.py [-h] -f str -o str -r str -a float [-m] [-L str]
Where:
  -h
     Print a short help message
  -f str
     Input file
  -o str
     output file
  -r str
     result file: output of the main program
  -a float
     rho: lower bound factor of likelihood
  -m
     allow multiple evolutions from germline (GL)
  -L str:
     method to solve LLH: cvxopt/pLP (default: cvxopt)

Example command python greedy_expand.py -f example.tsv -r example.txt -o example.full.txt -a 0.9

The output of the above command on the example input using the output generated above.