/usr/share/genometools/gtdata/sketch/default.style is in genometools-common 1.5.1-2ubuntu1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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This is the GenomeTools annotation viewer config file.
All options must be set inside the 'style' table.
All items in this table must be tables, called 'sections'.
Typically there is one section per feature type.
Color definitions
-----------------
Colors are given as RGB triplets
{red=<val>,green=<val>,blue=<val>(,alpha=<val>)}
where <val> is a decimal value between 0 and 1.
The alpha value is optional, as a default 0.5 will be used.
Global format settings
----------------------
Global settings, such as margins, spacers, etc. are found at the end of this
file, in the "format" section.
]]--
style =
{
gene = {
-- Color definitions
stroke = {red=0.0, green=0.0, blue=0.0, alpha = 1.0},
stroke_marked = {red=1.0, green=0.0, blue=0.0},
fill = {red=0.9, green=0.9, blue=1.0},
style = "box",
-- Collapsing options
collapse_to_parent = false,
split_lines = true,
-- Caption options
max_capt_show_width= nil,
-- Display this track only if the viewport is not wider than this
-- number of nucleotides. Set to 0 to disable type track.
max_show_width = nil,
},
--------------------------------------
mRNA = {
-- Color definitions
stroke = {red=0.0, green=0.0, blue=0.0, alpha = 1.0},
stroke_marked = {red=1.0, green=0.0, blue=0.0},
fill = {red=0.4, green=0.5, blue=0.6},
style = "box",
-- Collapsing options
collapse_to_parent = false,
split_lines = true,
-- Caption options
max_capt_show_width= nil,
-- Display this track only if the viewport is not wider than this
-- number of nucleotides. Set to 0 to disable type track.
max_show_width = nil,
},
--------------------------------------
exon = {
-- Color definitions
stroke = {red=0.0, green=0.0, blue=0.0, alpha = 1.0},
stroke_marked = {red=1.0, green=0.0, blue=0.0},
fill = {red=0.6, green=0.6, blue=0.9},
style = "box",
-- Collapsing options
collapse_to_parent = true,
split_lines = true,
-- Caption options
max_capt_show_width= nil,
-- Display this track only if the viewport is not wider than this
-- number of nucleotides. Set to 0 to disable type track.
max_show_width = nil,
},
--------------------------------------
CDS = {
-- Color definitions
stroke = {red=0.0, green=0.0, blue=0.0, alpha = 1.0},
stroke_marked = {red=1.0, green=0.0, blue=0.0},
fill = {red=0.9, green=0.9, blue=0.2},
style = "box",
-- Collapsing options
collapse_to_parent = true,
split_lines = true,
-- Caption options
max_capt_show_width= nil,
-- Display this track only if the viewport is not wider than this
-- number of nucleotides. Set to 0 to disable type track.
max_show_width = nil,
},
--------------------------------------
TF_binding_site = {
-- Color definitions
stroke = {red=0.0, green=0.0, blue=0.0, alpha = 1.0},
stroke_marked = {red=1.0, green=0.0, blue=0.0},
fill = {red=0.8, green=0.6, blue=0.6},
style = "box",
-- Collapsing options
collapse_to_parent = false,
split_lines = true,
-- Caption options
max_capt_show_width= nil,
-- Display this track only if the viewport is not wider than this
-- number of nucleotides. Set to 0 to disable type track.
max_show_width = nil,
},
--------------------------------------
intron = {
-- Color definitions
stroke = {red=0.0, green=0.0, blue=0.0, alpha = 1.0},
stroke_marked = {red=1.0, green=0.0, blue=0.0},
fill = {red=1.0, green=1.0, blue=1.0},
style = "caret",
-- Collapsing options
collapse_to_parent = true,
split_lines = true,
-- Caption options
max_capt_show_width= nil,
-- Display this track only if the viewport is not wider than this
-- number of nucleotides. Set to 0 to disable type track.
max_show_width = nil,
},
--------------------------------------
repeat_region = {
-- Color definitions
stroke = {red=0.0, green=0.0, blue=0.0, alpha = 1.0},
stroke_marked = {red=1.0, green=0.0, blue=0.0},
fill = {red=0.8, green=0.3, blue=0.3},
style = "box",
-- Collapsing options
collapse_to_parent = false,
split_lines = true,
-- Caption options
max_capt_show_width= nil,
-- Display this track only if the viewport is not wider than this
-- number of nucleotides. Set to 0 to disable type track.
max_show_width = 0,
},
--------------------------------------
LTR_retrotransposon = {
-- Color definitions
stroke = {red=0.0, green=0.0, blue=0.0, alpha = 1.0},
stroke_marked = {red=1.0, green=0.0, blue=0.0},
fill = {red=0.8, green=0.5, blue=0.5},
style = "box",
-- Collapsing options
collapse_to_parent = false,
split_lines = true,
-- Caption options
max_capt_show_width= nil,
-- Display this track only if the viewport is not wider than this
-- number of nucleotides. Set to 0 to disable type track.
max_show_width = nil,
},
--------------------------------------
long_terminal_repeat = {
-- Color definitions
stroke = {red=0.0, green=0.0, blue=0.0, alpha = 1.0},
stroke_marked = {red=1.0, green=0.0, blue=0.0},
fill = {red=0.9, green=0.9, blue=0.4},
style = "box",
-- Collapsing options
collapse_to_parent = true,
split_lines = true,
-- Caption options
max_capt_show_width= nil,
-- Display this track only if the viewport is not wider than this
-- number of nucleotides. Set to 0 to disable type track.
max_show_width = nil,
},
target_site_duplication = {
max_show_width = 0,
},
--------------------------------------
protein_match = {
-- Color definitions
stroke = {red=0.0, green=0.0, blue=0.0, alpha = 1.0},
stroke_marked = {red=1.0, green=0.0, blue=0.0},
fill = {red=0.1, green=0.1, blue=0.5},
style = "box",
-- Collapsing options
collapse_to_parent = true,
split_lines = true,
-- Caption options
max_capt_show_width= nil,
-- Display this track only if the viewport is not wider than this
-- number of nucleotides. Set to 0 to disable type track.
max_show_width = nil,
},
--------------------------------------
five_prime_cis_splice_site = {
collapse_to_parent = true,
},
--------------------------------------
five_prime_splice_site = {
collapse_to_parent = true,
},
--------------------------------------
three_prime_cis_splice_site = {
collapse_to_parent = true,
},
--------------------------------------
three_prime_splice_site = {
collapse_to_parent = true,
},
--------------------------------------
expressed_sequence_match = {
fill = {red=0.2, green=0.2, blue=0.8},
max_show_width = 10000,
max_num_lines = 10,
max_capt_show_width= 5000,
},
--------------------------------------
binding_site = {
fill = {red=0.7, green=0.2, blue=0.8},
max_show_width = 10000,
max_num_lines = 10,
max_capt_show_width= 10000,
},
--------------------------------------
SNP = {
fill = {red=0.1, green=0.8, blue=0.8},
max_show_width = 10000,
max_num_lines = 10,
max_capt_show_width= 10000,
},
--------------------------------------
deletion = {
fill = {red=0.1, green=0.8, blue=0.8},
max_show_width = nil,
max_num_lines = 10,
max_capt_show_width= 10000,
},
--------------------------------------
chromosome = {
fill = {red=0.1, green=0.8, blue=0.8},
max_show_width = nil,
max_num_lines = 10,
},
--------------------------------------
substitution = {
fill = {red=1.0, green=0.1, blue=0.05},
max_show_width = 10000,
max_num_lines = 10,
max_capt_show_width= 1000,
},
--------------------------------------
BED_feature = {
fill = {red=0.0, green=0.1, blue=0.0},
style = "box",
},
--------------------------------------
BED_thick_feature = {
fill = {red=0.0, green=0.5, blue=0.0},
style = "box",
collapse_to_parent = true,
},
--------------------------------------
BED_block = {
fill = {red=0.0, green=1.0, blue=0.0},
style = "box",
collapse_to_parent = true,
},
--------------------------------------
GC_content = {
-- this is for a custom track
stroke = {red=0.2, green=0.2, blue=1.0, alpha = 0.4},
},
--------------------------------------
-- Defines various format options for drawing.
format =
{
-- Set the following three settings to 'false' to globally disable them.
split_lines = true, -- generally enable splitting
show_block_captions = true, -- generally show captions
show_track_captions = true, -- generally show track captions
margins = 30, -- space left and right of diagram, in pixels
bar_height = 16, -- height of a feature bar, in pixels
bar_vspace = 10, -- space between feature bars, in pixels
track_vspace = 15, -- space between tracks, in pixels
ruler_font_size = 8, -- size of scale labels
ruler_space = 20, -- space between ruler and first track
block_caption_font_size = 8, -- size of block captions
block_caption_space = 7, -- space between blocks and their captions
track_caption_font_size = 8, -- size of track captions
track_caption_space = 7, -- space between tracks and their captions
arrow_width = 6, -- width of feature arrowheads, in pixels
stroke_width = .5, -- width of outlines, in pixels
unit = "bp", -- basepair unit, e.g. "bp"
ruler_left_text = "5'", -- text left of the ruler axis
ruler_right_text = "3'", -- text right of the ruler axis
stroke_marked_width = 1.5, -- width of outlines for marked elements, in pixels
show_grid = true, -- shows light vertical lines for orientation
min_len_block = 20 , -- minimum length of a block in which single elements are shown
track_title_color = {red=0.7, green=0.7, blue=0.7, alpha = 1.0},
default_stroke_color = {red=0.1, green=0.1, blue=0.1, alpha = 1.0},
background_color = {red=1.0, green=1.0, blue=1.0, alpha = 1.0},
},
}
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