p3-gto-dna

Extract DNA from a GTO

p3-gto-dna.pl [options] gtoFile

This script reads one or more locations from the standard input and outputs the corresponding DNA from the input GenomeTypeObject file.

Parameters

The positional parameter should be the name of the GenomeTypeObject file in JSON format.

The standard input can be overridden using the options in Input Options. The standard input should contain location strings in the key column (specified using Column Options) and the region name in the column identified by the --label parameter.

Location strings are of the form contigID_start+len for the forward strand and contigID_start-len for the backward strand.

Additional command-line options are as follows.

  • fasta

Output should be in FASTA format, with the region name as the ID.

  • label

Index (1-based) or name of the column containing the region names. The default is the first column (1).