Releases: NBISweden/AGAT
AGAT-v1.4.0
AGAT-v1.3.3
What's Changed
Full Changelog: v1.3.2...v1.3.3
AGAT-v1.3.2
/!\ Please avoid to use that version ! Important bug for files with only level3 features (exons, CDS) when recreating Level2 (mRNA) and level1 (gene) - stop prematurely
What's Changed
- Rendering :
- Re-activting progress bar (tata has been deactivated by mistake in previous releases)
- Display AGAT header for all scripts (before was only for sp scripts)
- Providing log information to user about the config file taken.
- fix #441 use L3 feature instead to L1 as template to create features when transcript_id exists by @Juke34 in #442. Bug was affecting GTF input annotations that have only level3 features (CDS,exons;etc.) and that was outputted in GTF (GFF output are fine excepted their transcript_id attribute that become wrong but are anyway useless in GFF).
Full Changelog: v1.3.1...v1.3.2
AGAT-v1.3.1
What's Changed
- Fix #435 agat_sp_compare_two_annotations.pl now output gene IDs by @Juke34 in #437
- Fix #436 agat_sp_manage_functional_annotation.pl now appending Name,product,dbxref,product attributes by default instead of replacing. Add parameters to clean those attributes. by @Juke34 in #438
Full Changelog: v1.3.0...v1.3.1
AGAT-v1.3.0
What's Changed
- Clean_clone by @Juke34 in #384 : add a clean_clone function to clean GFF feature while cloning it (e.g. when used as a template to create another feature). add clean_attributes_from_template parameter in agat_config.yaml to activate it.
- fix #383 by @Juke34 in #402 : -agat_convert_sp_gff2bed.pl was throwing
Can't "continue" outside a when block
error when using -nc parameter - fix #389 by @Juke34 in #403: fix a case that ended up with feature wihtout ID and add test
- fix nex readthedocs requirements by @Juke34 in #414
- New script to move feature from features of a same record (agat_sp_move_attributes_within_records) by @Juke34 in #413
- agat_sp_manage_IDs.pl not sorting feature consistently fix #411 by @Juke34 in #415
- agat_sp_separate_by_record_type.pl not sorting features consistently by @Juke34 in #423
- fix 424 - bug in agat_sp_complement_annotations.pl / check_feature_overlap_from_l3_to_l1 by @Juke34 in #425
- update agat_sp_add_start_and_stop.pl by @Juke34 in #429. Now handle GTF case (stop codon out of the CDS), allow CDS extension to find the first start/stop codon, and possibility to skip codon with IUPAC nucleotide to avoid NNN to be seen as a start or stop codon.
- Update doc by @Juke34 in #432
Full Changelog: v1.2.0...v1.3.0
AGAT-v1.2.0
new scripts:
- agat_sp_add_intergenic_regions.pl
- agat_sp_add_splice_sites.pl
Update/fix:
- agat_convert_minimap2_bam2gff.pl : fix #363 save AS information from BAM into GFF score (instead of phase) and put a dot for the phase
- Update statistics rendering (e.g. agat_sp_statistics.pl): Avoid to display twice stats when there is no isoform, add "(bp)" to clarify what means the numbers.
- new features in feature_levels.yaml :
- pseudogenic_region
- pseudogenic_cds
- intergenic_region
- protein_bind
- regulatory
- five_prime_cis_splice_site
- three_prime_cis_splice_site
- remove JSON from MYMETA.yml
- fix #346 : config.yaml is now called by default agar_config.yaml. It is now possible to create one at the fly with a chosen name. It is also possible to call all script specifying a config file located and named as wished.
- fix #368 - Avoid seq_id 0 to be replaced by default SEQ value
- fix #378 - fix auto format detection for sq scripts
- homogenize input/ouput
- use exclusively AGAT::BioperlGFF (_sq_script was using Bio::Tools::GFF for input/output; sp script were using AGAT::BioperlGFF for input and Bio::Tools::GFF for output)
- improving AGAT::BioperlGFF to take care of GFF and GTF output (adding parameter VERSION and TYPE). Remind AGAT::BioperlGFF is an improved version of Bio::Tools::GFF
- simplify code by factorizing OmniscientToGTF.pm and BioperlGFF.pm by implementing redundant function into BioperlGFF (e.g. filtering feature by GTF version; _gff25_string_JD and _gff25_string to fix incorrect GTF output provided by bioperl, etc)
new test:
- agat_convert_minimap2_bam2gff.pl
- agat_sq_add_attributes_from_tsv.pl
- agat_sp_add_intergenic_regions.pl
- agat_sp_add_splice_sites.pl
doc:
- remove 0 from agat config file which is not a correct to select for GTF version
- remove agat_sq_manage_ID from doc (official script is agat_sq_manage_IDs)
- update pod (removing option not used)
- update doc .md
AGAT-v1.1.0
- Update readme
- add the AGAT version in the log using the AGAT header method
- doc:
- fix #297 modify output name/type
- #303 revise gfx doc for clarity
- #300 add new script agat_sq_rename_seqid.pl in order to rename sequence identifiers.
- add feature types in feature_levels.yaml: 3'-utr, 5'-utr, crispr, splice3, splice5
- fix #329 - when creating L1 from L2 be sure the L1 ID used is not already used by a feature of another type.
- fix #327 - avoid crash if CDS less than 3 nt in agat_sp_filter_incomplete_gene_coding_models.pl
- fix #325 and improve related merge functions (see improved result of test gff_syntax 15). Fix error in keep_only_uniq_from_list2 function to merge identical isoform and add merge_ suffix for merged attributes
- fix #315 add skip_merge_l3 in feature_levels yaml file to handle which feature to skip at the check_all_level3_locations step (decide which type of feature to merge when overlapping)
- fix #290 - deal with GeMoMA peculiar case where L3 is attached to L1 while L2 exists while L2 is also attached to L1. Parent attribute used as a locus_tag
- fix #347 update end location only if longest
- fix #350 improve AGAT to deal properly with peculiar Exonerate gff
- fix #352 do not check feature when already removed from hash in merge_overlap_loci to avoid error
Code:
- factorize functions _merge_overlap_features and merge_overlap_features to keep only the later
- change miscCount uniqID and uniqIDtoType hashes into a single hash for code simplification
- remove L1 and L2 for newly created IDs. Fix problem ID use several times in e.g. agat_sp_prokka_fix_fragmented_gene_annotations_1.gff output file (used by tRNA level1 gene created)
- Improve check_gene_overlap_at_CDSthenEXON to work at l2 and l1 if no children, and rename it into check_feature_overlap_from_l3_to_l1.
- add get_uniq_id function to make unique ID on the fly for spread features that can share identical IDs
- use push in infosequential instead of omniscient for Push-L3-omiscient-3: level3 - Use Unique ID even for CDS to avoid confusion in location and level3 checks - remove strand when cloning L3 to create a l2 (see issue #350)
AGAT-v1.0.0
AGAT version1.0.0 … it implies lot of changes:
· Add a script called agat, allowing to access feature_levels file, access and modify configuration file, list the tools, see the AGAT version being used, etc.
· 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) in 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
AGAT-v0.9.2
- agat_convert_sp_gff2gtf.pl - fix #245 by making CDS identifier uniq using start and stop position on to of ID because they can share a same ID
- agat_sp_extract_sequences.pl - fix #246 : Remove name from header (now use --keep_attributes and the original attribute tag will be use instead ). Add --keep_attributes and --keep_parent_attributes to keep information from GFF into the fasta. Update test accordingly.
- New script agat_sq_reverse_complement.pl - fix #248
- add missing dependency LWP::Protocol::https dependency used to catch SO on the fly from URI/URL - fix #260
- update doc
AGAT-v0.9.1
- Fix #242 - error due to inefficient loop over topfeatures and standalone features.
- Re-activate genome coverage statistics
- remove plurial in sentences of statistics output
- increase time efficiency of agat_sp_statistics.pl - e.g. compute only once the genome size, only once the topfeatures and standalone feature statistics ...