make_prg

A tool to create and update PRGs for input to Pandora from a set of Multiple Sequence Alignments.

Table of Contents

• Dependencies
• Install
  • No installation needed - precompiled portable binary
  • pip
• Running on a sample example
• Usage

Dependencies

make_prg has two commands: from_msa and update. The update command requires MAFFT to be in your PATH. It can be installed:

1. from source: https://mafft.cbrc.jp/alignment/software/;
2. using conda: conda install -c bioconda mafft;

Install

No installation needed - precompiled portable binary

You can use make_prg with no installation at all by simply downloading the precompiled binary, and running it. In this binary, all libraries are linked statically.

• Requirements:

  • GLIBC >= 2.17 (present on Ubuntu >= 13.04, Debian >= 8.0, CentOS >= 7, RHEL >= 7.9, Fedora >= 19, etc);

• Download:

  wget https://github.com/leoisl/make_prg/releases/download/v0.3.0/make_prg_0.3.0
  

• Running:

chmod +x make_prg_0.3.0
./make_prg_0.3.0 -h

• Credits:

  • Compilation is done using PyInstaller.

• Notes:

  • We provide precompiled binaries for Linux OS only;

pip

• Requirements: python>=3.7

• Installing:

pip install git+https://github.com/leoisl/make_prg

• Running:

make_prg -h

Running on a sample example

To see how to input files to both make_prg from_msa and make_prg update, and the outputs they create on a sample example, see sample example.

Usage

$ make_prg --help
usage: make_prg <subcommand> <options>

Subcommand entrypoint

optional arguments:
  -h, --help     show this help message and exit
  -V, --version  show program's version number and exit

Available subcommands:
  
    from_msa     Make PRG from multiple sequence alignment dir
    update       Update PRGs given new sequences output by pandora.

from_msa

$ make_prg from_msa --help
usage: make_prg from_msa

optional arguments:
  -h, --help            show this help message and exit
  -i INPUT, --input INPUT
                        Input dir: all files in this will try to be read as the supported alignment_format. If not aligned in fasta alignment_format, use -f to input the alignment_format type
  -o OUTPUT_PREFIX, --output_prefix OUTPUT_PREFIX
                        Output prefix: prefix for the output files
  -t THREADS, --threads THREADS
                        Number of threads
  -f ALIGNMENT_FORMAT, --alignment_format ALIGNMENT_FORMAT
                        Alignment format of MSA, must be a biopython AlignIO input alignment_format. See http://biopython.org/wiki/AlignIO. Default: fasta
  --max_nesting MAX_NESTING
                        Maximum number of levels to use for nesting. Default: 5
  --min_match_length MIN_MATCH_LENGTH
                        Minimum number of consecutive characters which must be identical for a match. Default: 7
  -v, --verbose         Increase output verbosity

update

$ make_prg update --help
usage: make_prg update

optional arguments:
  -h, --help            show this help message and exit
  -u UPDATE_DS, --update_DS UPDATE_DS
                        Filepath to the update data structures. Should point to a file *.update_DS.
  -d DENOVO_PATHS, --denovo_paths DENOVO_PATHS
                        Filepath containing denovo sequences output by pandora. Should point to a denovo_paths.txt file.
  -o OUTPUT_PREFIX, --output_prefix OUTPUT_PREFIX
                        Output prefix: prefix for the output files
  -t THREADS, --threads THREADS
                        Number of threads
  --mafft MAFFT         Path to MAFFT executable. By default, it is assumed to be on PATH
  --keep_temp           Keep temp files.
  -v, --verbose         Increase output verbosity