Make a file with all allele details for QC pipeline

[kimrutherford]

• gene ID
• gene name
• allele ID
• allele name
• allele type
• allele description
• references, separated by commas

[kimrutherford]

I've added an exporter for allele details but I found a problem: the alleles in Chado don't have a publication/reference attached because we haven't needed it before. So the exporter can't export the refs. I'll fix the allele loading code to store the reference but it will delay things a bit. I should be able to implement it on Monday.

Here's an example of how the export file looks at the moment with no references:
https://curation.pombase.org/kmr44/allele-details-example.tsv

[kimrutherford]

I'll fix the allele loading code to store the reference

That's done now. So after tonight's load we should be able to export a full file of allele details from Chado, including the references.

[kimrutherford]

So after tonight's load we should be able to export a full file of allele details from Chado, including the references.

That seemed to work:
https://curation.pombase.org/dumps/builds/pombase-build-2023-08-14/exports/all-allele-details.tsv
https://curation.pombase.org/dumps/latest_build/exports/all-allele-details.tsv

@manulera please let me know if you find any problems

[manulera]

Hi @kimrutherford. Sorry it took me a while to get to this, could you add a column with the allele_synonym?

Ignore that. I will not use it

[manulera]

Hi @kimrutherford, I have updated the pipeline so that it uses that file.

[kimrutherford]

Hi @kimrutherford, I have updated the pipeline so that it uses that file.

Thanks!

Is this the file that should be processed by the nightly load to read transvar coordinates for storing in Chado?:
allele_qc/results/allele_results_transvar.tsv

[manulera]

Yes, exactly, and the equivalent exists for the protein modifications as well.

[ValWood]

Is this still current?

[kimrutherford]

Still need to do this bit:

Is this the file that should be processed by the nightly load to read transvar coordinates for storing in Chado?:
allele_qc/results/allele_results_transvar.tsv

Yes, exactly, and the equivalent exists for the protein modifications as well.