rPFP

This repository is the current and maintained version of Recursive PFP from https://github.com/marco-oliva/r-pfbwt. That repository is now depreceated. Any issues should be posted here.

rPFP is a tool to build the run-length encoded BWT and the SA values at the run heads from the prefix-free parsing of the input data.

Docker

rPFP is available on docker:

docker pull moliva3/r-pfbwt:latest
docker run moliva3/r-pfbwt:latest rpfbwt --help

If using singularity:

singularity pull rpfbwt_sif docker://moliva3/r-pfbwt:latest
./rpfbwt_sif rpfbwt --help

Build

rPFP can be built using:

git clone git@github.com:EddieFerro/rPFP.git
cd rPFP
mkdir build && cd build
cmake ..
make -j

How to use rPFP

rPFP takes as input the prefix-free parse of the input data, namely a dictionary D₁ and a parse P₁, and the dictionary D₂ and the parse P₂ obtained by prefix-free parsing P₁. Note that rPFP does not use P₁, it only uses D₁, D₂ and P₂. In order to compute the prefix-free parsing of the input data we can use pfp++ (link here). The following example computes the run-length encoded BWT of multiple sequences of yeast.

wget https://gitlab.com/manzai/Big-BWT/-/raw/f67022fe74dae0234e516324103613a0fdd58a6e/yeast.fasta?inline=false -O ./yeast.fasta
pfp++ -f yeast.fasta -w 10 -p 100 --output-occurrences 
pfp++ -i yeast.fasta.parse -w 5 -p 11 
rpfbwt  --l1-prefix yeast.fasta --w1 10 --w2 5 --threads 10

Usage

We report here all the available parameters for rPFP

rpfbwt
Usage: rpfbwt [OPTIONS]

Options:
  -h,--help                   Print this help message and exit
  --l1-prefix TEXT REQUIRED   Level 1 Prefix.
  --w1 UINT REQUIRED          Level 1 window length.
  --w2 UINT REQUIRED          Level 2 window length.
  -t,--threads UINT           Number of threads.
  --chunks UINT:INT in [1 - 1000]
                              Number of chunks.
  --integer-shift UINT        Integer shift used during parsing.
  --tmp-dir TEXT:DIR          Temporary files directory.
  --bwt-only                  Only compute the RLBWT. No SA values.
  --version                   Version number.
  --configure                 Read an ini file