Big gene_presence_absence file

Question

Big gene_presence_absence file

Opened this issue 7 years ago · 3 comments

Hello! I am trying to use phandango for getting a tree against the gene presence absence matrix from Roary. It all worked fine when I had smaller data sets, but now I have more genomes and a larger gene presence absence file (250 MB). When I try loading the csv, the site crashes (I tried with Chrome and Firefox). Is there a way to fix this? Thank you :)

Answer 1 · 2017-03-13T07:29:25.000Z

James have a simple python script here which minimises this file

Answer 2 · 2017-03-13T12:52:28.000Z

Thank you! Now I can load everything, but phandango crashes when I try to export a svg file. Do you maybe know how to solve this?

Answer 3 · 2017-04-20T17:46:10.000Z

Hi @ivaatanas - i'm guessing that the file is just too large to be handled by the code we use to construct the SVG. Perhaps @simonrharris can solve this, but I would suggest using screenshots as I think this will be extremely hard to fix (SVGs with millions of tiles would be really hard to work with as well).
Thanks, james