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gamcil / clinker

Gene cluster comparison figure generator
MIT License
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Clinker issue: Blocks instead of arrows #89

Open clpas opened 1 year ago

clpas commented 1 year ago

When the Genbank input file contain their CDS information within 'join(...)', clinker does not work properly (see picture). Can anyone help me with this problem? Thanks!

Screenshot 2022-10-12 135151

gamcil commented 1 year ago

We handled this via email, but just for record keeping, this is caused by sequence features spanning the origin in circular sequence records. I implemented some functionality to try and automatically fix these scenarios (https://github.com/gamcil/clinker/commit/16f795f813fb8f29ca4382df0efebcd797be9031) which will be in the next release. However, it will be better to manually adjust the origin/linearise your sequence externally (e.g. in Geneious/SnapGene/UGENE etc) before giving it to clinker.

pweigele commented 1 year ago

this happens to some files after changing the origin for circular phage genomes using Geneious. if you replace the line containing the first instance of the word "join" with source 1..{genome length} and then delete the line containing the second instance of the word "join" that fixes the block issue. however, you lose that feature where the second instance of the word join occurs. p.s. this is one of the most useful and elegant tools I have come across, thank you!!!