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)

AGAT-v0.3.0

• Add new script agat_convert_minimap2_bam2gff.pl

• Add new feature type in json files

• Add function activate_warning_limit in utilities

• Add test for agat_convert_minimap2_bam2gff.pl (and add minimap sam and bam files for future tests)

• Add gff_syntax test 35

• Add warnings when no phase specified within the CDS and enhance how we deal with cds phase in case of no phase at all

• Add option to remove offset in agat_sp_extract_sequences.pl to deal with offset even when we do not translate the sequence.

• Add log file for omniscient (activated by default for agat_convert_sp_gxf2gxf.pl) and polish logging messages

• Rename agat_sp_to_tabulated.pl to agat_convert_sp_gff2tsv.pl and fix it (number of column can vary now and we put N/A when info not applicable for the feature.)

• Rename Change agat_sp_split_by_level2_feature.pl into agat_sp_separate_by_record_type.pl because now deal with topfeature and standalone features.

• Rename agat_sq_manage_ID.pl into agat_sq_manage_IDs.pl

• Remove constant LEVEL1 LEVEL2 etc in OmniscientI

• Remove redundant info (topfeature dedicated hash. Info already exists in the value of other->level->level1). Create new function to access to json values stored into omniscient and adapt scripts accessing topfeatures.

• Remove agat_sp_gxf_to_gff3.pl because the same as agat_convert_sp_gxf2gxf.pl. It allows to avoid to take care of this 2 scripts in parallel.

• Fix potential problem for agat_sp_filter_feature_by_attribute_* because features were removed from omniscient while we looped over in the same time.

• Fix agat_sp_compare_two_BUSCOs.pl to deal with BUSCOv4 too

• Fix #33 #34 #35 #38 #40

• Fix typo and update pod/help

• Update AGAT to deal with standalone features (l1 without children. Before it was removing them). Modify test files and scripts to include those standalone features.

• Update agat_sp_statistics.pl add number of overlapping genes within the statistics. Update to take topfeature and standalone features into account.

• Update ontology to use complete one instead of SOFA within AGAT

• Move JSON related code to OmniscientJson.pm

• Use of OntologyEngineI in OmniscientI.pm to filter ontology terms to follow the GFF3 rules: Feature type must be sequence_feature (SO:0000110) or an is_a child of it.

AGAT-v0.2.3

• new script: agat_convert_sp_gff2zff.pl
• script name modified: agat_convert_sp_gxf_to_gxf.pl to agat_convert_sp_gxf2gxf.pl
• update pods

AGAT-v0.2.2

• improve agat_convert_bed2gff.pl to re-create CDS too (default behaviour)
• improve agat_convert_sp_gff2gtf.pl to be able to select output among all GTF versions available + update help
• fix error message when json file fails to load
• improve agat_sp_kraken_assess_liftover.pl to deal with output in a non-local file.
• update README

AGAT-v0.2.1

fix wrong calculation in the script agat_convert_sp_gff2bed.pl

AGAT-v0.2.0

Fixes:
#22 update printSurrounded to avoid line truncation
#23 agat_sq_basic_statistics.pl, add parameter to inflate multi-parent features
#24 agat_sp_extract_sequences.pl, now deals with seq < 3 nucleotide or empty translation
#25 update message in agat_sp_merge_annotations.pl
#27 add converter agat_convert_genscan2gff.pl

New scripts:
agat_convert_sp_gff2gtf.pl
agat_convert_sp_gxf_to_gxf.pl (copy of agat_sp_gxf_to_gff3.pl)
agat_convert_embl2gff.pl
agat_convert_mfannot2gff.pl
agat_convert_sp_gff2bed.pl
agat_sp_kraken_assess_lift_coverage.pl
agat_convert_genscan2gff.pl

Updates:
update features_level.json to handle more ensembl feature types

• esthetic changes
  fix STDOUT for agat_sp_filter_feature_by_attribute_presence.pl
  fix CDS starting offset in agat_sp_extract_sequences (translation in protein was wrong if starting CDS phase was different than 0. We clip now 1 or 2 nucleotide when needed to start in the correct frame)
  add test for the new scripts
  update OmniscienI to deal with no_check_skip option as an array + lower case key in uniqID hash + deal differently in _check_l2_linked_to_l3 to better create l2 feature (update gff_syntax test case9 to reflect the change).
  ...

AGAT-v0.1.1

• fixing agat_sq_mask.pl script
• Update README.md
• update tests
• update script helps
• fix #16
• fix #15
• add gff syntax case 33 and case 34 (to be compatible with the weird gff from nf-core dataset)
• add transcription_end_site in features_level3.json
• fix lowercase ID to stay uppercase when uppercase ID are created by the Omniscient constants

AGAT-v0.1.0

• Fix #6,#7,#8,#9,#10,#11
• 5 new scripts:
  agat_sp_filter_feature_by_attribute_value.pl
  agat_sp_compare_two_annotations.pl
  agat_sp_compare_two_BUSCOs.pl
  agat_sp_sensitivity_specificity.pl
  agat_sp_filter_feature_by_attribute_value.pl (to replace maker_select_models_by_AED_score.pl from GAAS repo. It is standardised here that make it able to perform more advance tasks)
• Modification of agat_sp_manage_IDs.pl to get shorter default ID naming. The previous style is still available with the --ensembl option
• add tests
• Improve/fix output path and names for some scripts
• cosmetic changes: Clean code, improve help, factored some code (moved into utilities mod

AGAT-v0.0.3

Create utilities module for clarity.
Add function get_proper_codon_table to check codon table because previous version of bioperl set codon table to 1 even is 0 is asked.
Update of all script that use codon table, and update the output of agat_sp_fix_longest_ORF.pl that was varying depending bioperl version used. => this fix the test step problem in bioconda
fix typo.