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
python plot_LST_vXX.py id f l -a
python plot_LST_vXX.py id f l -c
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.