Luis M Rodríguez-R
and 1 contributors

NAME

Bio::Polloc::LocusIO::gff3 - A LocusIO for Gff3

DESCRIPTION

A repeatitive locus.

IMPLEMENTS OR EXTENDS

AUTHOR - Luis M. Rodriguez-R

Email lmrodriguezr at gmail dot com

APPENDIX

Methods provided by the package

new

Creates a Bio::Polloc::LocusIO::gff3 object.

Returns

A Bio::Polloc::LocusIO::gff3 object.

gff3_line

Formats the locus as a GFF3 line and returns it.

Arguments

-force

Boolean (1 or 0)

Returns

The GFF3-formatted line (str) =head3 Note

This function stores the line in cache. If it is called twice, the second time will return the cached line unless the -force=1> flag is passed.

INTERNAL METHODS

Methods intended to be used only within the scope of Bio::Polloc::*

_next_locus_impl

_write_locus_impl

_gff3_attribute

Properly escapes an attribute for GFF3 (an attribute the value of one of the colon-separated entries in the ninth column)

Purpose

To simplify the code of Bio::Polloc::LocusI::gff3_line

Arguments

The value to escape

Returns

The escaped value

_gff3_value

Properly escapes a value on the GFF3 line. I.e., the content of one column. Not to be used with the ninth column, because scapes the colon. the comma and the equals signs. Use instead the _gff3_attribute function attribute by attribute

Purpose

To simplify the code of gff3_line

Arguments

The value to escape

Returns

The escaped value

_gff_decode

Decodes the URI-fashioned values on GFF3

Arguments

The value to decode (str)

Returns

The decoded value (str)