AGAT-v0.9.0

• 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

AGAT-v0.8.1

• 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

AGAT-v0.8.0

• remove R and R::Statistics from default dependencies because were problematic for conda and because it was heavy while it was not so much used. If needed, it has to be installed aside.
• update doc
• Fix #97 (agat_convert_sp_gff2bed.pl) add --nc parameter to handle non-coding L2 features
• fix #150 - add information in troubleshooting section about problem related to long sequence line in fasta file
• fix #147 (agat_sp_manage_functional_annotation.pl ) remove dash value from Interpro output
• fix #157 (agat_sp_manage_functional_annotation.pl). Better logging message and fix Regex for PE=
• fix #162 (agat_sp_manage_functional_annotation.pl). Copy the Name, product, Ontology_term, Dbxref and uniprot_id attributes from mRNA to the CDS.
• fix #165 (agat_sp_fix_fusion.pl and agat_sp_fix_overlaping_genes.pl) use the feature instead of the gene_id when calling check_gene_positions to be able to work with any level1 feature type. (AGAT was searching the gene_id for the gene feature type only)
• fix #168 (agat_sp_filter_feature_from_kill_list.pl) check no other l2 linked to l1 before to remove l1
• fix #172 (agat_convert_sp_gxf2gxf.pl). Call --expose without gff input file was crashing.

AGAT-v0.7.0

• Dramatically speed up the parser in special invocation of the check l3 linked to l1

• Fix #103 ( agat_sp_manage_functional_annotation)

• Fix #108 (agat_sp_manage_functional_annotation)

• add test for agat_sp_manage_functional_annotation

• fix #128 Add warning when l2 not on same seq_id than its parent. Fix check_level1_positions to avoid to update location when L2 not on same seq_id than its parent.

• fix #129

• fix #135 for agat_convert_bed2gff.pl : wrong id was used for strand and score resulting in wrong strand in output

• fix #139 fix if else statement to accept csv

• fix #143 IDs not numbering properly in agat_sp_manage_IDs.pl

• add new script agat_sq_count_attributes.pl to check attributes without modifying the file

• speedup the script agat_sq_keep_annotation_from_fastaSeq.pl

• rename agat_sq_keep_annotation_from_fastaSeq.pl into agat_sq_filter_feature_from_fasta.pl

• Update pod and fix misspellings

• Move CI from travis to github actions

AGAT-v0.6.2

• move wiki to doc and update documentation for readthedocs (https://agat.readthedocs.io/en/latest/?badge=latest)
• add a progress bar
• fix wrong UTR created when CDS has ribosomal slippage.
• Fix #119 Improve gff sensor. Wrong parser used when special character was among values of attributes (e.g. = ).
• Fix #117 Overlap can be now checked when one locus has a CDS and the other one no CDS (but same l2 feature type).
• Fix GTF parsing. AGAT store in memory GFF format. When converting GTF to GFF the stop codon was not included within the CDS. Now it can deal with stop codon starting a new exon (a CDS is created) and even spliced stop-codon.
• Fix agat_converter_sp_gff2gtf.pl. When stop codon is starting an exon or splitter over 2 exons, a piece of CDS was left while should have been removed. Now the converter deals properly with this edge case.
• Improve parsing. Now twice faster.

AGAT-v0.6.1

fix #110 intron missing 1bp in calculation for agat_sp_statistics.pl
fix #111 import missing for plot is statistics.pm (agat_sp_statistics.pl -p)
improvement of extract_sequeces.pl:
--cdna gives now real cdna. Add --mrna option to get biological mRNA.
Remove DONOTREVCOMP option (that was acting only on minus strand feature).
Add revcomp parameter that acts on all features (minus or plus strand).
Now only spreads feature are merged together (before it was all L3 features).
Add --merge to be able to merge features not spread (e.g. exon).
Add option plus_strand_only to get sequence only from plus strand (minus strand feature are revcomp). Update help.

AGAT-v0.6.0

• New script: agat_sq_manage_attributes.pl - allows to play on attribute in sequential mode
• New script: agat_sp_filter_feature_from_keep_list.pl - to filter feature according to a list
• New script agat_sp_filter_gene_by_intron_numbers.pl - to filter gene by intron numbers (Fix #95)
• New script agat_sp_filter_record_by_coordinates.pl - to filter gene by coordinates (fix #73)
• New script agat_sp_filter_gene_by_length.pl - to filter gene by length
• Fix #94 newly created gene feature with comon tag used for ID instead of new nbis labeled one when no L2 no L1 case
• Fix #104 add moose among dependencies in the readme
• Add new feature types in the json files to be compliant with refseq
• Add new paragraph within the troubleshooting section of the readme

AGAT-v0.5.1

Update Readme, add a troubleshooting paragraph
Fix #83 in agat_convert_sp_gff2gtf.pl: remove stop codon from the CDS when converting to GTF (works only if stop_codon feature exists)
Fix #82 add parameter to translate alternative start codon by a M in agat_sp_extract_sequences.pl
Fix #78 fix mispelling in statistics report
Fix #80 Update Help in agat_sp_flag_premature_stop_codons.pl
Fix #77 bug in agat_convert_sp_gff2bed.pl. When several isoform only one is printed
Fix #75 add verbosity for a specific message in OmniscientI.pm
Fix ID when several similar blast name in agat_sp_manage_functional_annotation.pl
Fix #71 log file based on input file
Fix #69 fix the --expose option in agat_convert_sp_gxf2gxf.pl that was not working anymore (to display the json files)
add lncrna in features_level2.json

AGAT-v0.5.0

Fix #49 #50 #51 #54 #55 #58 #60 #62 #63 #64 #65 #66 #67 #68
Merge PR #61

• add new script: agat_sp_flag_premature_stop_codons.pl agat_sp_filter_feature_from_kill_list.pl agat_sp_prokka_fix_fragmented_gene_annotations.pl
• add new parameter --cp to agat_sp_manage_attributes.pl
• update and modify features_level1.json,features_level2.json,features_level3.json files
• locus tag attribute provided by the user now overwritte the default list instead to be appended
• add test 36 in gff_syntax
• add tests for new scripts
• new attachedL2Sequential hash to keep track of the link between l2 and l1 features when sequential.
• fix typo

AGAT-v0.4.0

• add new script agat_sq_add_attributes_from_tsv.pl (Fix #44)
• fix regression introduced in AGAT-v0.3.0 that involved high slowness in statistics (issue #45 and #43 ).
• Update agat_convert_sp_gff2gtf.pl (Fix #46) => fix GTF output by skipping bioperl. Now all attribute's values are quoted and gene_id and transcript_id attributes come first in the attribute list.
• do not change output name anymore in agat_sq_manage_IDs.pl (keep name provided by the user intact)
• Fix link in Readme (PR #42)