在「JCVI教程」编码序列或蛋白序列运行共线性分析流程（上）还是有一个尴尬的事情，就是只用到两个物种，不能展示出JCVI画图的方便之处，因此这里参考https://github.com/tanghaibao/jcvi/wiki/MCscan-(Python-version)的分析，只不过画图部分拓展下思路。
首先要运行如下代码获取目的数据
python -m jcvi.apps.fetch phytozome Vvinifera,Ppersica,Tcacao
python -m jcvi.formats.gff bed --type=mRNA --key=Name Vvinifera_145_gene.gff3.gz -o grape.bed
python -m jcvi.formats.gff bed --type=mRNA --key=Name Ppersica_139_gene.gff3.gz -o peach.bed
python -m jcvi.formats.gff bed --type=mRNA --key=Name Tcacao_233_gene.gff3.gz -o cacao.bed
python -m jcvi.formats.fasta format --sep="|" Vvinifera_145_cds.fa.gz grape.cds
python -m jcvi.formats.fasta format --sep="|" Ppersica_139_cds.fa.gz peach.cds
python -m jcvi.formats.fasta format --sep="|" Tcacao_233_cds.fa.gz cacao.cds
# find ortholog
python -m jcvi.compara.catalog ortholog grape peach --cscore=.99
python -m jcvi.compara.catalog ortholog peach cacao --cscore=.99
# build .simpe
python -m jcvi.compara.synteny screen --minspan=30 --simple grape.peach.anchors grape.peach.anchors.new
python -m jcvi.compara.synteny screen --minspan=30 --simple peach.cacao.anchors peach.cacao.anchors.new
然后按照教程的配置文件进行画图
layout文件内容如下
# y, xstart, xend, rotation, color, label, va, bed
.7, .2, .4, 45, , Grape, top, grape.bed
.5, .2, .8, 0, , Peach, top, peach.bed
.7, .4, .8, -45, , Cacao, bottom, cacao.bed
# edges
e, 0, 1, grape.peach.anchors.simple
e, 1, 2, peach.cacao.anchors.simple
seqids文件内容如下
chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19
scaffold_1,scaffold_2,scaffold_3,scaffold_4,scaffold_5,scaffold_6,scaffold_7,scaffold_8
scaffold_1,scaffold_2,scaffold_3,scaffold_4,scaffold_5,scaffold_6,scaffold_7,scaffold_8,scaffold_9,scaffold_10r
运行python -m jcvi.graphics.karyotype seqids layout会得到如下结果
三个物种的共线性图
我就在思考一个问题如何让他形成一个三角形。经过一波三角运算和不断尝试，我定义了如下的layout
# y, xstart, xend, rotation, color, label, va, bed
.5, 0.025, 0.625, 60, , Grape, top, grape.bed
.2, 0.2, .8, 0, , Peach, top, peach.bed
.5, 0.375, 0.975, -60, , Cacao, top, cacao.bed
# edges
e, 0, 1, grape.peach.anchors.simple
e, 1, 2, peach.cacao.anchors.simple
那么效果怎么样呢？运行python -m jcvi.graphics.karyotype seqids layout吧
凑合吧
当然这里只展示了，grape和peach, peach和cacao之间的共线性，我又想着能不能加上grape和caocao呢？我尝试着运行下面的代码，
python -m jcvi.compara.catalog ortholog grape cacao --cscore=.99
python -m jcvi.compara.synteny screen --minspan=30 --simple grape.cacao.anchors grape.cacao.anchors.new
并继续修改了layout
# y, xstart, xend, rotation, color, label, va, bed
.5, 0.025, 0.625, 60, , Grape, top, grape.bed
.2, 0.2, .8, 0, , Peach, top, peach.bed
.5, 0.375, 0.975, -60, , Cacao, top, cacao.bed
# edges
e, 0, 1, grape.peach.anchors.simple
e, 1, 2, peach.cacao.anchors.simple
e, 0, 2, grape.cacao.anchors.simple
运行python -m jcvi.graphics.karyotype seqids layout会得到如下结果
awesome
我觉得给我一点时间，我也能用JCVI画出下面的图了
amazing
