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jameshadfield / phandango

an interactive viewer for populations of bacterial genomes linked by a phylogeny
http://phandango.net
MIT License
118 stars 30 forks source link

Handle gffs with multiple contigs/chromosomes #75

Open simonrharris opened 8 years ago

simonrharris commented 8 years ago

This should be relatively simple - we'd need to read the ##sequence-region info at the top of the gff to define the lengths of each chromosome. This has been requested by team133, so it would also need to cope with much larger genomes. I'd suggest we put in a check and when zoomed out to beyond a certain level (e.g. a certain number of bp or features to be shown) we just show an overview of the chromosomes.

simonrharris commented 8 years ago

Having the chromosome positions would also give us something to display in the mini genome top left

jameshadfield commented 8 years ago

Cool. Maybe team133 could drive some development?

I think it's conceptually easy but would require a lot of work in reality as all the data structures, display components and file parsers involved would change.

As this would facilitate larger genomes I think it should be first tested on a single concatenated dataset to see how slow it is, as other tricks such as database storage / server side stuff may be needed which is a much bigger endeavour.

jameshadfield commented 8 years ago

fixed at a4e2250 @simonrharris ?

Or is there a checklist of things still to do?