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gamcil / clinker

Gene cluster comparison figure generator
MIT License
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Renaming coding sequence back to gene number #110

Open timeresistance1996 opened 5 months ago

timeresistance1996 commented 5 months ago

Hi @gamcil ,

Clinker helps excellent visualization of gene comparisons. However, I encounter a slight issue when using the Identity/Similarity output. How can I rename the coding sequences back to gene numbers?

code clinker 1_2.gff 1_1.gff -o clinker.out

error: [14:50:20] WARNING - Could not find parent gene of 1_1. Using coding sequence coordinates instead. [14:50:20] WARNING - Could not find parent gene of 1_2. Using coding sequence coordinates instead.

output $ head clinker.out 1_2 vs 1_1

Query Target Identity Similarity cf905c13-59a1-48fa-93da-e2074e048ddb a9c8c031-1b68-41bb-9303-35cb41674d1f 0.63 0.63
7f2eb39f-2337-40eb-87ad-8f650ca39158 ab28d9d1-b904-4a5f-b67d-24cf95c58a92 1.00 1.00
0e1a809f-e5d7-4d15-bb77-fdc927289453 00075d31-ceb7-4e04-ab93-4cc9b5f00211 1.00 1.00

gamcil commented 5 months ago

Could you upload one of the GFF files you are using here?

timeresistance1996 commented 5 months ago

Yes, this is header of the 1_2.gff i used which is generated by Prodigal.

1_2_gff.txt

gamcil commented 5 months ago

Looks like the error was clinker not looking for uppercase ID fields. This should be fixed with clinker v0.0.29.