NBISweden/AGAT: AGAT-v1.0.0

AGAT version1.0.0 … it implies lot of changes: · Add a script call agat, allowing to access feature_levels file, access and modify configuration file, list the tools and see the AGAT version being used. · Use of AppEaser module from https://github.com/polettix/App-Easer to create a multi layers help in agat script · Replace feature_level json files by a single yaml file · Apparition of a configuration file (config.yaml) allowing to tune behaviour of all scripts (input, output, AGAT parsing etc... /!\ For sq scripts the config can only modify input/output format behaviours). · As there is now a config file, superfluous params removed in some scripts (particularly in gxf2gxf) · Make gtf output possible to every sp script via config.yaml and create a dedicated module (OmniscientToGTF) based on code from the gff2gtf script. · Create a BioperlGFF module based on the Bioperl code to correct parse GFF/GTF files when they contain a mix of GFF1 and GFF2/GFF3 like seen in Augustus and Tsebra output files (fix #288). Add corresponding tests · Modify name of the Module Omniscient by AGAT · Modify all scripts to load config before starting "my $config = get_agat_config();" · Modify all scripts to take in consideration the output format set the config · Centralize and standardize the creation of new text file and gff file in OmniscientO with prepare_file and out prepare_gffout. Will not overwrite an existing file.

Other modifications · Fix header issue (newline missing) ing gff2gtf conversion · Fix GTF1 that was not really selectable in gff2gtf · Code from gff2gtf script has been moved within OmniscientToGTF module · fix the script compare_annotations by rewriting it from scratch. + add tests · Add new features in levels (lot of EDTA ones #271) and others e.g. "Contig", "expressed_sequence_match"," transcription_start_site" · agat_sp_manage_functional_annotation.pl : Avoid dash in output when no GO term #272 · Updating warning messages to be more precise #273