Published April 5, 2024 | Version v1.4.0
Software Open

NBISweden/AGAT: AGAT-v1.4.0

Creators

  • 1. IRD

Description

  • fix #448 an issue affecting AGAT when using GFF2 and GFF2.5 bioperl parser. Bioperl is adding an extra empty ID attribute that mess up with AGAT. An extra step in AGAT remove this empty attribute and allows AGAT to works appropriately.
  • 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).
  • 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

Files

AGAT-1.4.0.zip

Files (25.4 MB)

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md5:8492f74f35a48153d6329d618d74705a
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Additional details

Related works

Is supplement to
https://github.com/NBISweden/AGAT/tree/v1.4.0 (URL)