参考：
https://blog.csdn.net/u012110870/article/details/102804593
https://www.jianshu.com/p/1658e702ba17
首先查看一下gff文件和CDS文件的对应情况，有的gff文件没有transcript_id这个注释。
比如我的就没有
python -m jcvi.formats.gff bed --type=mRNA --key=Name T_ant_maker.final.gff > T.bed
python -m jcvi.formats.gff bed --type=mRNA --key=Name A_aqu_genome.final.gff > A.bed
···
如果没有CDS文件，就自己提取
gffread in.gff3 -g ref.fa -x cds.fa
···
python -m jcvi.formats.fasta format --sep="|" T_ant_cds.fa T.cds
python -m jcvi.formats.fasta format --sep="|" A_aQU_cds.fa A.cds
python -m jcvi.compara.catalog ortholog T A --cscore=.99（画个点图看看共线性）
python -m jcvi.compara.synteny screen --minspan=30 --simple T.A.anchors T.A.anchors.new
或者不加参数：python -m jcvi.compara.synteny screen --simple T.A.anchors T.A.anchors.new
python /home/spider/project/yuantao/script/hoptop_scripts/simple2links.py T.A.anchors.simple
python /home/spider/project/yuantao/script/simple2links.py A.T.anchors.simple
T.A.anchors.simple_link.txt文件就可因用来画圈图了，你也可以把里面每个染色体的共线性区块保存成一个文件，后面画不同的颜色。
类似上图1号染色体的复制粘贴放一个文件，2号染色体的复制粘贴放一个文件，以此类推。
circos.conf文件，每个染色体区块单独设置颜色。
karyotype=karyotype.Aaqu.txt,karyotype.Tant.txt
chromosomes_units = 100000
<ideogram>
<spacing>
default = 0.005r
<pairwise Aaqu01;Tant13>
spacing = 6r
</pairwise>
</spacing>
radius = 0.90r
thickness = 6p
fill = yes
stroke_color = 160,32,240
stroke_thickness = 2p
show_bands = no
show_label = yes
label_font = default
label_radius = dims(ideogram,radius) + 0.05r
label_size = 9
label_parallel = yes
label_fromat = eval(sprintf("%s",var(chr)))
</ideogram>
<links>
bezier_radius=0r
bezier_radius_purity=0.75
color=set2-8-qual-1
crest=0.5 ##以上几列为links的全局的设置，包括连线的弯曲度，颜色
<link>
file = chr1_color.txt ##1号染色体的共线性文件
radius = 0.85r
color = green_a2
bezier_radius_purity = 0.2
thickness=2 ##连线的厚度
z=20 #层数
crest = 1
</link>
<link>
file = chr2_color.txt ##2号染色体的共线性文件
radius = 0.85r
color = red
bezier_radius_purity = 0.2
thickness=2 ##连线的厚度
z=20 #层数
crest = 1
</link>
<link>
file = chr3_color.txt ##3号染色体的共线性文件
radius = 0.85r
color = purple
bezier_radius_purity = 0.2
thickness=2 ##连线的厚度
z=20 #层数
crest = 1
</link>
<link>
file = chr4_color.txt
radius = 0.85r
color = black
bezier_radius_purity = 0.2
thickness=2 ##连线的厚度
z=20 #层数
crest = 1
</link>
<link>
file = chr5_color.txt
radius = 0.85r
color = vvdblue
bezier_radius_purity = 0.2
thickness=2 ##连线的厚度
z=20 #层数
crest = 1
</link>
<link>
file = chr6_color.txt
radius = 0.85r
color = orange
bezier_radius_purity = 0.2
thickness=2 ##连线的厚度
z=20 #层数
crest = 1
</link>
<link>
file = chr7_color.txt
radius = 0.85r
color = vvdpurple
bezier_radius_purity = 0.2
thickness=2 ##连线的厚度
z=20 #层数
crest = 1
</link>
<link>
file = chr8_color.txt
radius = 0.85r
color = vvdred
bezier_radius_purity = 0.2
thickness=2 ##连线的厚度
z=20 #层数
crest = 1
</link>
<link>
file = chr9_color.txt
radius = 0.85r
color = 255,255,0
bezier_radius_purity = 0.2
thickness=2 ##连线的厚度
z=20 #层数
crest = 1
</link>
<link>
file = chr10_color.txt
radius = 0.85r
color = 255,204,0
bezier_radius_purity = 0.2
thickness=2 ##连线的厚度
z=20 #层数
crest = 1
</link>
<link>
file = chr10_color.txt
radius = 0.85r
color = 153,153,30
bezier_radius_purity = 0.2
thickness=2 ##连线的厚度
z=20 #层数
crest = 1
</link>
<link>
file = chr11_color.txt
radius = 0.85r
color = 255,153,0
bezier_radius_purity = 0.2
thickness=2 ##连线的厚度
z=20 #层数
crest = 1
</link>
<link>
file = chr12_color.txt
radius = 0.85r
color = 255,204,204
bezier_radius_purity = 0.2
thickness=2 ##连线的厚度
z=20 #层数
crest = 1
</link>
<link>
file = chr13_color.txt
radius = 0.85r
color = 102,102,0
bezier_radius_purity = 0.2
thickness=2 ##连线的厚度
z=20 #层数
crest = 1
</link>
radius=0.40r
thickness=1
</links>
show_ticks = yes
show_tick_labels = yes
<ticks>
radius = 1r
color = black
thickness = 2p
multiplier = 1e-6
<tick>
spacing = 5u
size = 10p
</tick>
<tick>
color = black
thickness = 4p
spacing = 5u
size = 10p
show_label = yes
label_size = 10p
label_offset = 10p
format = %d
</tick>
</ticks>
<image>
dir* = .
radius* = 500p
<<include etc/image.conf>>
</image>
<<include etc/colors_fonts_patterns.conf>>
<<include etc/housekeeping.conf>>
