NBISweden/AGAT: AGAT-v0.8.1

Published January 10, 2022 | Version v0.8.1

Software Open

improve doc + pod
Fix problem of the GFF sensor due to tabulation among attributes #176
Fix agat_sp_sensitivity_specificity.pl script that was not working properly
avoid error if no output provided for agat_sp_extract_attributes.pl
Getting output of agat_sp_filter_record_by_coordinates.pl in seperate gff3 files #196
agat_sp_manage_functional_annotation.pl fix #192 : simplify name from blast. No _iso suffix and avoid to concat gene name for getting uniq gene name. Now we get a list of gene names.
agat_sp_fix_features_locations_duplicated.pl #204. Script re-written to modify a minimum the gene models (1bp removed in UTR) and when a case cannot be fixed, it is mentioned to the user (e.g. no UTR so cannot modify the gene model).
Now accept .gz input file #206
Fix bug #207: A bug was touching files without Level1 (gene) and level2 (transcript/mRNA) features, and only common tag. It was behaving well only for the first feature met and then it was no able to collect Isoform under the same gene feature.
agat_convert_sp_gxf2gxf.pl add no_progessbar parameter
agat_convert_sp_gxf2gxf.pl: keep embeded fasta in the gff by default #206 (but fasta can be thrown with the throw_fasta parameter)
agat_convert_embl2gff.pl improved to be able to deal .embl flat file made for submission with EMBLmyGFF3 (--emblmygff3 parameter)
#202 Increase the usage of combined assignment operators
happy new years 2022 - AGAT presented at PAG XXIX the 09/01/2022

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