NAME

coords2gff.pl - convert mummer coords files to gff3 format

SYNOPSIS

    # store results in OUTPUT.gff3
    perl coords2gff.pl [OPTIONS] <MUMMER_ALIGNMENT.coords> <OUTPUT.gff3>

    # print results to standard output
    perl coords2gff.pl [OPTIONS] <MUMMER_ALIGNMENT.coords>
    # or
    perl coords2gff.pl [OPTIONS] <MUMMER_ALIGNMENT.coords> -

DESCRIPTION

This script converts mummer output in coords files to gff3 formatted output.

OPTIONS

Alternative option names are separated by "|".

--switch-query-reference|switch|s

Take the query (2nd sequence in the alignment) as reference and the reference (1st sequence in the alignment) as query. Adjust coordinates accordingly.

--help|h|?

Complete help.

SEE ALSO

Bio::FeatureIO, Bio::SeqFeature::Generic

AUTHOR

jw bargsten, <joachim.bargsten at wur.nl>