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
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)