search

gamcil / clinker

Gene cluster comparison figure generator
MIT License
507 stars 66 forks source link

[Feature request] option to indicate subsection of Genbank file #62

Open dutchscientist opened 3 years ago

dutchscientist commented 3 years ago

Often we have a (prokka-generated) Genbank file, but only want to use a small subsection of it in Clinker. I don't know how easy it would be, but could an option be introduced to say xxxxx.gbk(133310-136309) so that only that region and the annotation are used?

dutchscientist commented 3 years ago

https://twitter.com/RoyChaudhuri/status/1375493280951988229

This solves it at the level of generating the input file (thanks Roy!), but is it a functionality useful for Clinker to have included?

gamcil commented 3 years ago

Hi @dutchscientist, sorry for taking so long to get back to this, pretty time poor at the moment. I remember from Twitter the --ranges argument wasn't working for you, do you still have the files/output from when you tried it before?

dutchscientist commented 3 years ago

No worries, very little time myself. There are no outputs as the program just "hangs", and after 10 minutes or so I gave up. It works well with the previous script to make the inputs files with Roy Chadhuri's script.