plot_LST

Basic use

python plot_LST_vXX.py id f l

where

• f is int, first line in .lst file
• l is int, last line in .lst file
• id being the name of a replicon in the gembase format : ggee.000.c00.00

If an id.config file exist, it will color the genes as many colors as there are classes in the .config file which is formatted as follow :

GENE001c01 classe1
GENE002c01 classe2
GENE003c01 classe1

with annotations

python plot_LST_vXX.py id f l -a

circular representation

python plot_LST_vXX.py id f l -c

On a tree

python plot_LST_vXX.py id_tree -t

with -t option, an id_tree.treeconfig file is needed, and is formatted as follow :

id1 f1 l1
id2 f2 l2
id3 f3 l3

where idx are names of leaves in the necessary i_tree.tree file, in Newick format, like :

((id1,id2),id3)

id_tree is the name of the tree.

To colorize genes, one .config file is needed where all desired genes from all classes are concatenated in it.