read_gb loses part of plasmid feature that spans across the start site

[Dobrokhotov1989]

Hi there,

I've spotted a bug in the reading gbk file where a feature spans across the plasmid "start". In the gbk it looks like this:

 CDS             join(4891..5096,1..751)
                     /note="pLannotate"
                     /label="TurboID"
                     /database="snapgene"
                     /identity="100.0"
                     /match_length="99.7"
                     /fragment="False"
                     /other="CDS"

but when read by read_gb() it only 'remembers' the first part, i.e. 4891..5096.

This file is used in the example: 559763_pLann.txt

library(plasmapR)
my_plasmid <- '559763_pLann.txt'
read_gb(my_plasmid) %>%
  plot_plasmid()

I would appreciate it if you could take a look

[BradyAJohnston]

Thanks for flagging this. You are right that I currently haven't taken in to account features that will go over the 'origin' of the plasmid. I will have to have a think about how to handle this, as just having the features start and end on the correct places won't work nicely with ggplot.

[BradyAJohnston]

Is there a particular reason that the origin point for the plasmid is in this location? I can think of a solution that would basically be changing the origin point for all of the features to be a different location in the plasmid, that doesn't overlap with a feature. I figure this will be the easiest approach. I might not do it for the parsing step, but it might be something that can be done in the plotting stage.

[Dobrokhotov1989]

Thanks Brady for the swift reply. There is no particular reason for origin being in the middle of a feature - it is just as I got plasmid sequencing results.