Changes for version 1.1 - 2012-04-13
- Changed the default API of Bio::GFF3::LowLevel::Parser to support multi-loc features. In order to be able to group feature lines that hand in some cases it would not be possibleave the same ID attribute, it now returns arrayrefs that are groups of the formerly-returned hashrefs.
- HOWEVER, there is a backward-compatibility layer that back-converts the features to the conform to the return types in 1.1. Existing users of this code should not be adversely affected.
- Add better support for Derives_from: feature line hashrefs now have a derived_features attribute holding an arrayref of the features that Derives_from this one.
- Remove assumptions in the parser about child features coming after their parents in the file. The GFF3 specification does not require this.
Changes for version 1.10 - 2014-02-28
- Removed dependency on forking and IO::Pipe for handling implicit FASTA section starts. Should fix problems on Windows. Thanks to Francisco Ossandon for the fix!
Documentation
make GFF3 from fasta sequences
Modules
fast, low-level functions for parsing and formatting GFF3
a fast, low-level gff3 parser
compatibility layer to support Bio::GFF3::LowLevel::Parser 1.0 API
make gff3 for the sequences in a fasta file
insert sync (###) directives into an existing GFF3 file. WARNING: this module does not really work in the general case, read the DESCRIPTION section below.