MCScanX2figure

mcscanx2figure.py

63:/data1/alima90/py/mcscanx2figure.py

Visualizing tool for MCScanX synteny block using SVG

1. 1. README
   2. command
   3. python mcscanx2figure.py gff_file_of_left_species_in_mcscanx gff_file_of_right_species_in_mcscanx mcscanx_file(collinearity) block_number > output.svg
   4. if you want to highlight link, add your genes in highlight_gene_list like
   5. highlight_gene_list = ['geneA','geneB']
   6. You can also change color of element such as gene, link and backborn.
   7. You can use RGB color as well as common color name

1. 3################################# USER SETTING PARAMETER ############################################

highlight_gene_list = ['Glyma12g04390'] backborn_color = 'rgb(135,206,250)' a_gene_color = 'blue' b_gene_color = 'blue' link_color = 'pink' link_opacity = 0.7 highlight_link_color = 'red' highlight_link_opacity = 0.7

mcscanx2figure_schematic.py

63:/data1/alima90/py/mcscanx2figure_schematic.py

Visualizing tool for MCScanX synteny block as schematic figure using SVG

1. 1. README
   2. command
   3. python mcscanx2figure_schematic.py gff_file_of_left_species_in_mcscanx gff_file_of_right_species_in_mcscanx mcscanx_file(collinearity) block_number > output.svg
   4. if you want to highlight link, add your genes in highlight_gene_list like
   5. highlight_gene_list = ['geneA','geneB']

1. 3################################# USER SETTING PARAMETER ############################################

highlight_gene_list = ['Glyma12g04390'] backborn_color = 'rgb(135,206,250)' gene_length = 10 intergenic_scale = 5000 ## zoom out intergenic sequence scale into 1/x a_gene_color = 'blue' b_gene_color = 'blue' link_color = 'pink' link_opacity = 0.7 highlight_link_color = 'red' highlight_link_opacity = 0.7