Published April 5, 2022
| Version v.0.9.0
Software
Open
NBISweden/AGAT: AGAT-v0.9.0
- 1. Alcediag
- 2. Oregon State University
- 3. @EuPathDB
Description
- fix #230 add tabix sorting with parameter --tabix to agat_convert_sp_gxf2gxf.pl
- Update doc and log about how AGAT works when only level3 feature presents in file
- add extra info in the log about the read file (Number of line in file, number of comment lines, info if fasta is included, Number of features lines, number of feature type (3rd column))
- make a change to use the common tag as level1 feature ID when possible instead of one created on the fly (nibsL1-...).
- add features in json files to be compliant to with Araport11 annotation and VEuPathDB
- Update print_omniscient to use a hash to deal with parameters
- code refactoring in OmniscientI
- Fix #215 merge adjacent feature by default (e.g. exon or CDS)
- replace awk command by perl approach to read line number to set the progress bar. Function is called get_general_info in OmniscientI
- new scripts: agat_sp_add_attribute_shortest_exon_size.pl and agat_sp_add_attribute_shortest_intron_size.pl to add info to gene and mRNA about the size of the shortest exon/intron. Can be use to filter records with agat_sp_select_feature_by_attribute_value.pl later
- add PAG 2022 presentation
- Fix #222 - Fix --blast_evalue type from int to float in agat_sp_manage_functional_annotation.pl
- Merge attributes when Merging two annotations (e.g. OmniscientI.pm in _merge_overlap_features used when --merge_loci activated; agat_sp_merge_annotations.pl / agat_sp_fix_overlaping_genes.pl )
- agat_sp_fix_overlaping_genes.pl improved (change the way we loop over features) and test added
- add create_or_append_tag on OmniscientTool
- update doc
Files
NBISweden/AGAT-v.0.9.0.zip
Files
(24.7 MB)
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md5:fc02b43079d3d921ddd1fad3f4ce785e
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Additional details
Related works
- Is supplement to
- https://github.com/NBISweden/AGAT/tree/v.0.9.0 (URL)