Opened 4 months ago

Closed 2 months ago

#1025 closed enhancement (fixed)

Release exporter should support StringTie data

Reported by: nicklas Owned by: nicklas
Priority: major Milestone: Reggie v4.16
Component: net.sf.basedb.reggie Keywords:
Cc:

Description

The current implementation of the release exporter only supports Cufflinks data. There are several things that need to be diffent when exporting StringTie data.

  • The array design is different. No features have been imported to the database so the exporter may have to parse the GTF file (unless we simply can copy it as it is)
  • A different list of data files (files to export must be white-listed)
  • Expression data is not in a FPKM file. If we want to export an expression matrix, we need to get this from other files.

Change History (6)

comment:1 Changed 4 months ago by nicklas

  • Status changed from new to assigned

comment:2 Changed 4 months ago by nicklas

(In [4689]) References #1025: Release exporter should support StringTie? data

Fixed so that the exporter doesn't crash when trying to export StringTie data. Array design files and expression matrix files are created but empty. JSON files are created with "gene.tsv" and "transcript.gtf" white-listed for exporting.

This is only a temporary solution that needs more work before it can be used in production.

comment:3 Changed 2 months ago by nicklas

(In [4743]) References #1025 and #1034.

Removed check that all raw bioassays must use the same array design which means that it should be possible to create releases containing both StringTie and Cufflinks data. We can do this because we don't export the expression matrix anymore (#1034).

comment:4 Changed 2 months ago by nicklas

(In [4745]) References #1025: Release exporter should support StringTie? data

Updated the whitelisted files for StringTie rawbioassays and AlignedSequences. For the latter we check the raw bioassay type and assume that we always have StringTie+Hisat and Cufflinks+Tophat and never any other combination.

comment:5 Changed 2 months ago by nicklas

(In [4759]) References #1025: Release exporter should support StringTie? data

Fixes a NullPointerException when encountering a legacy Tophat alignment that doesn't have any files. The issue was that the DataFilesFolder annotation is null due to this and the script writer will yet try create a mkdir command for it.

We will now only enter this section if the filtered file list contains at least one file, and then a DataFilesFolder annotation is required.

comment:6 Changed 2 months ago by nicklas

  • Resolution set to fixed
  • Status changed from assigned to closed
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