Difference between revisions of "MCScanX2figure"
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=== Config file === | === Config file === | ||
left_species_gff_file_path = Brapa_197_gene.gff3.sort | left_species_gff_file_path = Brapa_197_gene.gff3.sort | ||
+ | |||
right_species_gff_file_path = Thalophila_173_gene.gff3.sort | right_species_gff_file_path = Thalophila_173_gene.gff3.sort | ||
+ | |||
highlight_gene_list = Bra002260,Bra002261 | highlight_gene_list = Bra002260,Bra002261 | ||
+ | |||
highlight_link_list = None | highlight_link_list = None | ||
+ | |||
backborn_color = rgb(135,206,250) | backborn_color = rgb(135,206,250) | ||
+ | |||
gene_length = 10 | gene_length = 10 | ||
+ | |||
## intergenic_scale : zoom out intergenic sequence scale into 1/x | ## intergenic_scale : zoom out intergenic sequence scale into 1/x | ||
+ | |||
intergenic_scale = 1000 | intergenic_scale = 1000 | ||
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arrow_size = 5 | arrow_size = 5 | ||
+ | |||
a_gene_color = blue | a_gene_color = blue | ||
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highlight_a_gene_color = red | highlight_a_gene_color = red | ||
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b_gene_color = blue | b_gene_color = blue | ||
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highlight_b_gene_color = red | highlight_b_gene_color = red | ||
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link_color = pink | link_color = pink | ||
+ | |||
link_opacity = 0.5 | link_opacity = 0.5 | ||
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highlight_link_color = red | highlight_link_color = red | ||
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highlight_link_opacity = 0.8 | highlight_link_opacity = 0.8 |
Revision as of 10:03, 10 October 2014
Contents |
mcscanx2figure.py
63:/data1/alima90/py/mcscanx2figure.py
Visualizing tool for MCScanX synteny block using SVG
README
Command |
---|
python mcscanx2figure.py gff_file_of_left_species_in_mcscanx gff_file_of_right_species_in_mcscanx mcscanx_file(collinearity) block_number > output.svg |
if you want to highlight link, add your genes in highlight_gene_list like
highlight_gene_list = ['geneA','geneB']
You can also change color of element such as gene, link and backborn.
You can use RGB color as well as common color name
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:/home/alima90/py/mcscanx2figure_schematic_v1.1.py
Visualizing tool for MCScanX synteny block as schematic figure using SVG
README
Command |
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python mcscanx2figure_schematic.py config_file mcscanx_file(collinearity) block_number > output.svg |
Config file
left_species_gff_file_path = Brapa_197_gene.gff3.sort
right_species_gff_file_path = Thalophila_173_gene.gff3.sort
highlight_gene_list = Bra002260,Bra002261
highlight_link_list = None
backborn_color = rgb(135,206,250)
gene_length = 10
- intergenic_scale : zoom out intergenic sequence scale into 1/x
intergenic_scale = 1000
arrow_size = 5
a_gene_color = blue
highlight_a_gene_color = red
b_gene_color = blue
highlight_b_gene_color = red
link_color = pink
link_opacity = 0.5
highlight_link_color = red
highlight_link_opacity = 0.8