version 2.1.0

This release includes:

• fixing bugs with the phase calculation for CDS features on the negative strand and multi-isoform models
• updating the error level of the error messages (INFO, WARNING, ERROR) according to issue #114, providing the error level in output files, and updating corresponding documentation
• migrating from Travis to Github Actions and adding tests on Windows

version 2.0.3

This release includes several minor bug fixes.

version 2.0.2

This release includes:

• several minor bug fixes;
• gzip support (thanks @ctcncgr!)
• documentation fixes (thanks for the pointer @adf-ncgr!)

version 2.0.1

This release includes bug fixes to gff3_fix.

version 2.0.0

This is the initial python3 release for the GFF3toolkit. It is compatible with python3, but not python2.7. Please use release v1.4.5 if you prefer to use python2.7.

version 1.4.5

This is the final python2.7 release for the GFF3toolkit.
This update includes:

• Fixes issue #85
• minor bug fixes

version 1.4.4

1. Add statistic file
2. Fix a bug in FAQ.md
3. Update README.md for statistic file

version 1.4.3

• Add user-defined example files
• Fix a bug in which gff3_merge failed if only -u2 file is given #70

version 1.4.2

• Fix the problem that package can't be built correctly through bdist_wheel

version 1.4.1

This release contains the following changes:

• now GFF3 toolkit supports Windows #41 and Mac #48 as well
• add a new argument for gff3_merge, --all #35
  • --all: auto-assignment replace tags for all transcript features. (default: Only automatically assign replace tags for the transcript without replace tags)
• add new arguments for gff3_sort, --sort_template and --isoform_sort #38
  • --sort_template: A file that indicates the sorting order of features within a gene model
  • --isoform: Sort multi-isoform gene models by feature type (default: False)
• add new argument for gff3_to_fastsa, --embedded_fasta #39
  • --embedded_fasta: Specify this option if you want to extract sequence from embedded fasta.
• remove old APIs #46

Bug fixes:

• fixed a bug in which gff3_fix failed if the phase of the first CDS is missing. Set the initial phase as 0, if phase missing. #40
• fixed a bug in which gff3_merge only gets the user-defined transcripts from -u1 file. Now, it will get the user-defined transcripts from both -u1 and -u2 files.
• fixed a bug in which gff3_to_fasta failed if the input gff3 file pass all the QC check without detecting any formatting error.