Joachim Bargsten > Bio-Gonzales-0.0544 > coords2gff.pl

Download:
Bio-Gonzales-0.0544.tar.gz

Annotate this POD

CPAN RT

Open  0
View/Report Bugs
Source   Latest Release: Bio-Gonzales-0.0549

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>

syntax highlighting: