nested

External tools

Program is using other external tools. Before usage make sure you have the following tools installed:

• LTR finder (v 1.05+) - http://www.mybiosoftware.com/ltr_finder-1-0-5-find-full-length-ltr-retrotranspsons-genome-sequences.html
• blastx (v 2.2.31+) - https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download
• genometools (v 1.5.8) with gt sketch - https://github.com/genometools/genometools

Install

chmod +x setup.sh
sudo ./setup.sh

Setting up the config

Before usage, config.yml needs to be set up:

• ltr paths - executable, prosite and tRNAdb
• ltr arguments
• gt sketch path
• gt sketch arguments
• blastx protein database (our database available at ... )
• blastx arguments

Note: config.yml is located by default in directory /etc/nested/.

Usage

Usage: nested-nester [OPTIONS] INPUT_FASTA

Options:
  -s, --sketch_only       If true, nesting is not computed. Genes are sketched
                          only from existing gff files.
  -d, --data_folder TEXT  Output data folder.
  --help                  Show this message and exit.

Usage: nested-generator [OPTIONS] INPUT_DB OUTPUT_DB

Options:
  -l, --baselength INTEGER        Baselength for generated elements.
  -i, --number_of_iterations INTEGER
                                  Number of iterations in generating.
  -n, --number_of_elements INTEGER
                                  Number of generated elements.
  -f, --filter                    Filter database and create new one with
                                  given output db path.
  -s, --filter_string TEXT        Filter entries by given string [ONLY
                                  RELEVANT WITH -filter OPTION].
  -o, --filter_offset INTEGER     LTR offset allowed [ONLY RELEVANT WITH
                                  -filter OPTION].
  -d, --data_folder TEXT          Output data folder.
  --help                          Show this message and exit.