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CHANGELOG.md

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Changelog

emapper2gbk v0.1.0 (2021-06-29)

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 (2020-09-08)

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 (2020-06-24)

Fix

  • Issue with version of setup.cfg with PyPI.

emapper_to_gbk v0.0.5 (2020-06-24)

Fix

  • Issue in long_description of setup.py with PyPI.

emapper_to_gbk v0.0.4 (2020-06-24)

Fix

  • Issue in long_description of setup.py with PyPI.

emapper_to_gbk v0.0.3 (2020-06-24)

Fix

  • Issue in long_description of setup.py with PyPI.

emapper_to_gbk v0.0.2 (2020-06-24)

Fix

  • Issue in long_description of setup.py with PyPI.

emapper_to_gbk v0.0.1 (2020-06-24)

First release of emapper2gbk

Features

  • emapper2gbk entrypoint
  • emapper2gbk genomic to create genbank from eggnog-mapper results and single organism (with or without GFF)
  • emapper2gbk metagenomic to create genbank from eggnog-mapper results and gene catalogue of a metagenome (with or without GFF)

Integration

  • Use Github Actions for CI
  • Release on PyPI