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.
This release modifies heavily
emapper2gbk. Thegenomicandmetagenomicsubcommands have been removed. From this release, emapper2gbk is divided in two subcommands:genesandgenomes. Thegenessubcommand 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). Thegenomessubcommand 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
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).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).-gtforemapper2gbk genomes:-gt cds_onlyif the GFF file contains only CDS information.--eteforemapper2gbk genomes: when searching for taxonomic ID instead of requesting the EBI, use the packageete3.--keep-gff-annotationforemapper2gbk genomes: keep theproductfield of the CDS in the GFF file into the genbank file.Modify
-fgargument of fasta nucleic sequences (for genes or genomes) by-fn.Fix
Remove
genomicandmetagenomicsubcommands.