genometools-scripts

This repository contains scripts written in the Lua language using the GenomeTools Lua bindings. This API makes it quite easy to process GFF3 annotations and connect them to the corresponding sequences.

Please look at gt-TEMPLATE for an example of how to write these scripts.

List of currently available scripts (use make readme to update)

gt-TEMPLATE

Do something with an input GFF.
Usage: gt ./gt-TEMPLATE <options> < infile.gff

Options:
  -h, --help    show this help message and exit
  -x            a boolean option
  -s SOMETHING  some string input

gt-bequeath

Adds a given parent attribute to all child features.
Usage: gt ./gt-bequeath <options> < infile.gff

Options:
  -h, --help    show this help message and exit
  -a ATTRIBUTE  attribute to pass on to children (default: Name)

gt-encseq-sample

Extract random substrings from a GtEncseq. 
Usage: gt ./gt-encseq-sample <options> indexname

Options:
  -h, --help   show this help message and exit
  -min=MINLEN  minimum length (default: 10)
  -max=MAXLEN  maximum length (default: 100)
  -s SEED      random seed (default: time)
  -n NUMSTR    number of substrings (default: 100)

gt-ltrclean

Keep only 'best' (smallest e-value) protein match per overlapping cluster from LTRdigest results.
Usage: gt ./gt-ltrclean <options> < infile.gff3

Options:
  -h, --help  show this help message and exit
  -type=TYPE  root type (default: LTR_retrotransposon)

gt-stripstop

Converts all genes with internal stop codons to pseudogenes.
Usage: gt ./gt-stripstop <sequence file> < infile.gff

Options:
  -h, --help  show this help message and exit
  -r          skip feature instead of making it a pseudogene

gt-toplevelize

Promote features of a given type to toplevel.
Usage: gt ./gt-toplevelize <options> <sequence> < infile.gff

Options:
  -h, --help  show this help message and exit
  -t TYPE     type to toplevelize