Difference between revisions of "MCScanX2figure"

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== mcscanx2figure.py ==
 
== mcscanx2figure.py ==
  
63:/data1/alima90/py/mcscanx2figure.py
+
63:/home/alima90/py/mcscanx2figure.py
[[File:88 scheme1.svg|thumbnail]]
+
 
 
'''<big>Visualizing tool for MCScanX synteny block using SVG</big>
 
'''<big>Visualizing tool for MCScanX synteny block using SVG</big>
 
'''
 
'''
 
+
[[File:Mc2f1.jpg|1000px|frameless|center]]
 
README
 
README
  
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! Command
 
! 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
+
| python mcscanx2figure.py config_file mcscanx_file(collinearity) block_number > output.svg
 
|}
 
|}
  
 +
=== Config file ===
 +
MCScanX2figure config file example
  
 
+
[[File:MC2F config.txt]]
if you want to highlight link, add your genes in highlight_gene_list like
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highlight_gene_list = ['geneA','geneB']
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You can also change color of element such as gene, link and backborn.
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You can use RGB color as well as common color name
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+
 
+
 
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=== USER SETTING PARAMETER ===
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highlight_gene_list = ['Glyma12g04390']
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backborn_color = 'rgb(135,206,250)'
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a_gene_color = 'blue'
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b_gene_color = 'blue'
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link_color = 'pink'
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link_opacity = 0.7
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highlight_link_color = 'red'
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highlight_link_opacity = 0.7
+
  
 
== mcscanx2figure_schematic.py ==
 
== mcscanx2figure_schematic.py ==
  
63:/data1/alima90/py/mcscanx2figure_schematic.py
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63:/home/alima90/py/mcscanx2figure_schematic_v1.1.py
  
 
'''<big>Visualizing tool for MCScanX synteny block as schematic figure using SVG</big>
 
'''<big>Visualizing tool for MCScanX synteny block as schematic figure using SVG</big>
 
'''
 
'''
 
+
[[File:Mc2fs2.jpg|1000px|frameless|center]]
 
README
 
README
  
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! Command
 
! Command
 
|-
 
|-
| 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
+
| python mcscanx2figure_schematic.py config_file mcscanx_file(collinearity) block_number > output.svg
 
|}
 
|}
  
  
if you want to highlight link, add your genes in highlight_gene_list like
+
=== Config file ===
 
+
MCScanX2figure_schematic config file example
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)'
+
 
+
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
+
[[File:MC2FS.docx|thumbnail]]

Latest revision as of 06:19, 17 December 2014

Contents

mcscanx2figure.py

63:/home/alima90/py/mcscanx2figure.py

Visualizing tool for MCScanX synteny block using SVG

Mc2f1.jpg

README


Command
python mcscanx2figure.py config_file mcscanx_file(collinearity) block_number > output.svg

Config file

MCScanX2figure config file example

File:MC2F config.txt

mcscanx2figure_schematic.py

63:/home/alima90/py/mcscanx2figure_schematic_v1.1.py

Visualizing tool for MCScanX synteny block as schematic figure using SVG

Mc2fs2.jpg

README

Command
python mcscanx2figure_schematic.py config_file mcscanx_file(collinearity) block_number > output.svg


Config file

MCScanX2figure_schematic config file example

File:MC2FS.docx