- 31.Brassica oleracea.main.data
chr - mt mt 0 360271 powderblue
- 31.Brassica oleracea.data
segdup00001 mt 173327 317876
segdup00001 mt 3294 147844
segdup00002 mt 345349 348953
segdup00002 mt 3605 1
segdup00003 mt 345349 345660
segdup00003 mt 173637 173327
...
- 31.Brassica oleracea.genes.1.labels
mt 101064 120791 nad5 color=black
mt 1124 3408 nad5 color=black
mt 431 778 orf115b color=black
mt 26567 26953 nad1 color=black
mt 333722 334921 nad1 color=black
mt 3623 7388 nad1 color=black
...
- 31.Brassica oleracea.genes.1.forward
mt 26567 26953 color=blue
mt 333722 334921 color=blue
mt 3623 7388 color=blue
mt 15354 15434 color=blue
mt 16102 16548 color=blue
mt 19880 20278 color=blue
...
- 31.Brassica oleracea.genes.1.reverse
mt 101064 120791 color=firebrick
mt 1124 3408 color=firebrick
mt 431 778 color=firebrick
mt 4661 6694 color=firebrick
mt 7626 8105 color=firebrick
mt 8163 8648 color=firebrick
...
- And the main configuration file
file_delim = \t
<colors>
<<include bb.colors.conf>>
</colors>
# colors from http://www.w3schools.com/html/html_colornames.asp
# which are the same as those used by bb.drawseq
<fonts>
<<include fonts.conf>>
</fonts>
<<include bb.ideogram.conf>>
<<include bb.ticks.conf>>
karyotype = "31.Brassica oleracea.main.data"
<image>
dir = .
file = "31.Brassica oleracea.png"
# radius of inscribed circle in image
radius = 1200p
background = white
# by default angle=0 is at 3 o'clock position
angle_offset = -90
24bit = yes
auto_alpha_colors = yes
auto_alpha_steps = 5
</image>
chromosomes_units = 1000
#spacing=1u
# right side;left side abbreviations
chromosomes = mt
chromosomes_display_default = no
chromosomes_radius = mt:1.0r
# Links (bezier curves or straight lines) are defined in <links> blocks.
# Each link data set is defined within a <link>.
# As with highlights, parameters defined
# in the root of <links> affect all data sets and are considered
# global settings. Individual parameters value can be refined by
# values defined within <link> blocks, or additionally on each
# data line within the input file.
<links>
z = 0
radius = 1.00r
bezier_radius = 0r
<link file1>
z = 4;
show = yes
ribbon = yes
color = blue_a3
thickness = 1
file = "31.Brassica oleracea.data"
record_limit = 5000
<rules>
</rules>
</link>
</links>
<plots>
<plot>
show = yes
type = tile
file = 31.Brassica oleracea.genes.1.forward
#layers = 15
layers = 1
layers_overflow = collapse
margin = 0.02u
thickness = 30
padding = 8
orientation = out
stroke_thickness = 0
#stroke_color = none
color = mediumblue
r0 = 1r
r1 = 1.2r
z = 9
background = no
</plot>
<plot>
show = yes
type = tile
file = 31.Brassica oleracea.genes.1.reverse
#layers = 15
layers = 1
layers_overflow = collapse
margin = 0.02u
thickness = 30
padding = 8
orientation = in
stroke_thickness = 0
#stroke_color = none
color = firebrick
r0 = 0.8r
r1 = 1r
z = 10
background = no
</plot>
<plot>
show = yes
type = text
file = 31.Brassica oleracea.genes.1.labels
color = black
r0 = 1.00r
r1 = 1.20r
show_links = yes
link_dims = 4p,30p,64p,4p,4p
link_thickness = 2p
link_color = black
# set label font size here
label_size = 12p
label_font = condensed
padding = 0p
rpadding = 0p
label_snuggle = yes
# shift label up to its height in pixels in the angular direction
max_snuggle_distance = 25r
snuggle_sampling = 2
snuggle_tolerance = 0.25r
snuggle_link_overlap_test = yes
snuggle_link_overlap_tolerance = 2p
snuggle_refine = yes
</plot>
</plots>
anglestep = 0.5
minslicestep = 10
beziersamples = 1000
debug = no
warnings = no
imagemap = no
# don't touch!
units_ok = bupr
units_nounit = n