Opened 7 years ago
Closed 7 years ago
#1025 closed enhancement (fixed)
Release exporter should support StringTie data
Reported by: | Nicklas Nordborg | Owned by: | Nicklas Nordborg |
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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 by , 7 years ago
Status: | new → assigned |
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comment:2 by , 7 years ago
comment:3 by , 7 years ago
comment:4 by , 7 years ago
(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 by , 7 years ago
(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 by , 7 years ago
Resolution: | → fixed |
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Status: | assigned → closed |
(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.