emapper2gbk v0.3.1

Fix

• issue with change of the URL for REST request to EBI.

Modify

• replace setup.py/setup.cfg with pyproject.toml.
• replace use of pkg_resources that will become deprecated.
• update authors.rst.
• update license year.
• update readme.

emapper2gbk v0.3.0

Modify

• gff-type option -gt cds_only modify to -gt CDS
• function gff_to_gbk in genomes_to_gbk.py : replace gff-type = cds_only case to gff-type = CDS or mRNA or gene

Add

• gff-type option (-gt): add mRNA and gene parameters. Allows the tool to use the IDs in "mRNA" or "gene" field in the gff to match the faa file IDs. To do so with the "CDS" field the parameter cds-only has been replaced by CDS.

emapper2gbk v0.2.1

Fix

• issue with pypi classifiers.

emapper2gbk v0.2.0

Add

• support for gmove and eggnog GFF format.

• error messages if GFF is empty or if there is no overlap between IDs contained in fastas, GFF and eggnog-mapper annotation files.

• error message when having a syntax issue with the obo file.

• the possibility to give as input a full taxonomic affiliations instead of only an organism name (issue #9). Thanks to @Chabname.

• changelog.

• comments and update readme.

Modify

• use gffutils region to speed up emapper2gbk.

Fix

• an issue allowing abbreviated option in command line arguments.
• issue when gene IDs were only numeric (issue #10).
• use gobasic_file after downloading it.
• numerous typos.

emapper2gbk v0.1.0

This release modifies heavily emapper2gbk. The genomic and metagenomic subcommands have been removed. From this release, emapper2gbk is divided in two subcommands: genes and genomes.
The genes subcommand can be used for a catalogue of genes (with a fasta file for gene nucleic acid sequence, a fasta file for the protein sequence and the eggnog-mapper annotaiton file).
The genomes subcommand can be user for genome (with a fasta file for genome sequences, one for protein sequences, the eggnog-mapper anntoation file and a GFF file).
The two subcommands can be used on single file or on folder containing multiple files.

The scripts files of emapper2gbk have been renamed according to these changes.

Add

• New subcommand emapper2gbk genes: subcommand to use for catalogue of genes (with three inputs: fasta of nucleic sequences of genes, fasta of amino acids sequences of proteins and the eggnog-mapper annotation file).
• New subcommand emapper2gbk genomes: subcommand to use for genomes (with four inputs: fasta of nucleic sequences of genomes (chromosomes sequences), fasta of amino acids sequences of proteins, the eggnog-mapper annotation file and a GFF file).
• New option -gt for emapper2gbk genomes: -gt cds_only if the GFF file contains only CDS information.
• New option --ete for emapper2gbk genomes: when searching for taxonomic ID instead of requesting the EBI, use the package ete3.
• New option --keep-gff-annotation for emapper2gbk genomes: keep the product field of the CDS in the GFF file into the genbank file.
• Add dbxref (Kegg, Bigg, Pfam and CAZ) to genbank.

Modify

• Replace -fg argument of fasta nucleic sequences (for genes or genomes) by -fn.
• Replace GPL license by LGPL license.
• Refactoring of the code of emapper2gbk.
• Update readme (add pictures, badges and modify text about new subcommands).

Fix

• Numerous issues with the format of the output of new version of eggnog-mapper.
• Issue with Preferred_name.
• Issue with GO Terms.

Remove

• Remove genomic and metagenomic subcommands.
• Remove unused files.

emapper_to_gbk v0.0.7

Fix

• Issue with replacement of Bio.Alphabet in Biopython 1.78. This version is compatible with both versions: old versions (with Bio.Alphabet) and new versions (without Bio.Alphabet).

emapper_to_gbk v0.0.6

Fix

• Issue with version of setup.cfg with PyPI.

emapper_to_gbk v0.0.5

Fix

• Issue in long_description of setup.py with PyPI.

emapper_to_gbk v0.0.4

Fix

• Issue in long_description of setup.py with PyPI.

emapper_to_gbk v0.0.3

Fix

• Issue in long_description of setup.py with PyPI.