Opened 26 hours ago

Last modified 91 minutes ago

#1616 new enhancement

Implement support for new annotation type categories

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: critical Milestone: Reggie v5.4
Component: net.sf.basedb.reggie Keywords:
Cc:

Description

BASE 3.20 has a new feature where more than one annotation type category can be linked to a given subtype where an annotation can be used to discriminate between them. See ​https://base.thep.lu.se/ticket/2329.

As an example we can divide the AlignedSequences subtype into 3 different categories with the help of the Pipeline annotation: RNAseq, WGS and sRNAseq where each category only contains the annotation types that are relevant for the given pipeline.

For other item types we can make similar sub-categories.

Change History (3)

comment:1 by Nicklas Nordborg, 24 hours ago

In 7876:

References #1616: Implement support for new annotation type categories

Added Pipeline as the subcategory annotation type to AlignedSequences.

comment:2 by Nicklas Nordborg, 23 hours ago

In 7877:

References #1616: Implement support for new annotation type categories

Added sub-categories for AlignedSequences. There are five different with some variations in annotations.

  • RNAseq: Pipeline=RNAseq/Hisat/StringTie
  • RNAseq/2023: Pipeline=RNAseq/Hisat/2023
  • RNAseq/Legacy: Pipeline=RNAseq/Legacy
  • WGS: Pipeline=DNA/Tumor/WGS, DNA/Normal/WGS
  • sRNA: Pipeline=sRNAseq

comment:3 by Nicklas Nordborg, 91 minutes ago

In 7879:

References #1616: Implement support for new annotation type categories

Added sub-categories for MergedSequences. There are three different with some variations in annotations.

  • RNAseq: Pipeline=RNAseq
  • WGS: Pipeline=DNA/Tumor/WGS, DNA/Normal/WGS
  • sRNA: Pipeline=sRNAseq


Also moved the category for MaskedSequences to the new system. It us only used by the RNAseq pipeline and they are all the same so a single category will do.

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