在「JCVI教程」編碼序列或蛋白序列運(yùn)行共線性分析流程（上）還是有一個(gè)尷尬的事情，就是只用到兩個(gè)物種，不能展示出JCVI畫圖的方便之處，因此這里參考https://github.com/tanghaibao/jcvi/wiki/MCscan-(Python-version)的分析，只不過(guò)畫圖部分拓展下思路。

首先要運(yùn)行如下代碼獲取目的數(shù)據(jù)

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進(jìn)行畫圖

layout文件內(nèi)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文件內(nèi)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

運(yùn)行python -m jcvi.graphics.karyotype seqids layout會(huì)得到如下結(jié)果

三個(gè)物種的共線性圖

我就在思考一個(gè)問(wèn)題如何讓他形成一個(gè)三角形。經(jīng)過(guò)一波三角運(yùn)算和不斷嘗試，我定義了如下的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

那么效果怎么樣呢？運(yùn)行python -m jcvi.graphics.karyotype seqids layout吧

湊合吧

當(dāng)然這里只展示了，grape和peach, peach和cacao之間的共線性，我又想著能不能加上grape和caocao呢？我嘗試著運(yùn)行下面的代碼，

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

并繼續(xù)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

運(yùn)行python -m jcvi.graphics.karyotype seqids layout會(huì)得到如下結(jié)果

awesome

我覺(jué)得給我一點(diǎn)時(shí)間，我也能用JCVI畫出下面的圖了

amazing

圖片來(lái)自于https://science.sciencemag.org/content/345/6199/950