需要看下Nip和9311的基因匹配的有多少，思来想去，blast还是有点缺陷的，可能匹配到其他染色i他，需要用gff来帮助定一下位。所以，用基因的共线性分析看起来更合适一点。
- 调查，mcscanx，jcvi两个。jcvi貌似更新一些，我也常用python，功能上可能更容易上手。
- 安装，jcvi，
利用python3.6安装jcvi，不指定python版本安装的是2.7，后面出问题了
conda create -n jcvi -c bioconda last jcvi python=3.6
换用docker，用docker的出图了，我认为这个更靠谱。但是docker文件夹得在本地。
我是win装linux虚拟机，然后吧文件夹挂载到raid服务器，但是文件格式问题搞了很久，最后还是重新回复了docker的文件位置，虚拟机本地硬盘。
docker网站下载一个带tag的jcvi 3.10的
docker pull quay.io/biocontainers/jcvi:1.4.15--py310hd6be1da_0
下载好之后，进入docker 镜像
准备文件
- cds文件
2.gff文件或bed文件
没了
放到一个文件夹。
如果是gff，转化成bed
#gff convert to bed
python -m jcvi.formats.gff bed --type=mRNA --key=transcript_id Oryza_sativa.IRGSP-1.0.48.gff3 -o Nip.bed
python -m jcvi.formats.gff bed --type=mRNA --key=transcript_id Oryza_indica.ASM465v1.48.chr.gff3 -o 9311.bed
这个地方如果bed文件种第
分析共线性区域，这条命令会生成一堆东西，包括last比对结果。
#identify blocks
python -m jcvi.compara.catalog ortholog Nip 9311 --no_strip_names
get synteny，生成simple文件
python -m jcvi.compara.synteny screen --minspan=30 --simple 9311.Nip.anchors 9311.Nip.anchors.new
prepare for seqid and layout file
plot synteny
python -m jcvi.graphics.karyotype seqid layout
最后结果：
屏幕截图 2024-11-07 171537.png
屏幕截图 2024-11-07 170129.png
python -m jcvi.compara.synteny depth --histogram Nip.9311.anchors
python -m jcvi.compara.synteny depth --histogram Nip.9311.lifted.anchors
屏幕截图 2024-11-08 110128.png
.simple文件中的每一行都是一个连锁块，有起始和终止Nip基因，然后是起始和终止9311基因，最后两列是分数和方向。
Os01t0100100-01 Os01t0978100-01 BGIOSGA002569-TA BGIOSGA000001-TA 5761 +
Os10t0100500-01 Os10t0162856-00 BGIOSGA032412-TA BGIOSGA032250-TA 358 +
Os10t0164500-00 Os10t0579600-01 BGIOSGA032579-TA BGIOSGA033506-TA 1931 +
Os11t0106400-01 Os11t0194100-01 BGIOSGA034647-TA BGIOSGA034978-TA 630 +
Os11t0205500-02 Os11t0256400-01 BGIOSGA034343-TA BGIOSGA034190-TA 284 +
Os11t0264200-01 Os11t0312400-01 BGIOSGA035085-TA BGIOSGA034092-TA 191 +
Os11t0427500-01 Os11t0437800-01 BGIOSGA034091-TA BGIOSGA034059-TA 54 +
Os11t0453600-00 Os11t0586300-01 BGIOSGA034056-TA BGIOSGA033741-TA 612 +
Os11t0594500-00 Os11t0604700-00 BGIOSGA033738-TA BGIOSGA035559-TA 73 -
Os11t0615600-01 Os11t0622800-00 BGIOSGA035610-TA BGIOSGA035636-TA 56 +
Os11t0625900-01 Os11t0640600-00 BGIOSGA035572-TA BGIOSGA033646-TA 71 +
Os11t0653300-01 Os11t0668300-00 BGIOSGA033606-TA BGIOSGA033577-TA 72 +
Os11t0672700-01 Os11t0687200-03 BGIOSGA033576-TA BGIOSGA033542-TA 68 -
Os11t0691100-00 Os11t0707700-01 BGIOSGA033541-TA BGIOSGA033507-TA 90 +
Os11t0100800-01 Os11t0152500-01 BGIOSGA036827-TA BGIOSGA036625-TA 400 +
Os12t0106000-01 Os12t0145700-01 BGIOSGA034647-TA BGIOSGA034500-TA 318 +
Os12t0100700-00 Os12t0257900-01 BGIOSGA036827-TA BGIOSGA037229-TA 917 +
Os12t0277400-01 Os12t0641500-01 BGIOSGA036385-TA BGIOSGA035747-TA 1352 +
Os12t0258200-01 Os12t0277000-01 BGIOSGA018541-TA BGIOSGA018489-TA 85 +
Os02t0100100-01 Os02t0450000-01 BGIOSGA007319-TA BGIOSGA008132-TA 1735 +
Os02t0453500-01 Os02t0834300-01 BGIOSGA006534-TA BGIOSGA009360-TA 2774 +
Os03t0100010-00 Os03t0862100-01 BGIOSGA011641-TA BGIOSGA014002-TA 5047 +
Os04t0225100-01 Os04t0234600-01 BGIOSGA009378-TA BGIOSGA009362-TA 33 +
Os04t0100300-00 Os04t0126600-00 BGIOSGA015745-TA BGIOSGA015685-TA 137 +
Os04t0127200-02 Os04t0169666-00 BGIOSGA015814-TA BGIOSGA015606-TA 147 +
Os04t0171800-01 Os04t0198733-00 BGIOSGA015538-TA BGIOSGA015997-TA 108 -
Os04t0201200-01 Os04t0218600-02 BGIOSGA015603-TA BGIOSGA015929-TA 73 +
Os04t0243700-01 Os04t0693400-00 BGIOSGA015490-TA BGIOSGA014021-TA 3131 +
Os05t0100100-01 Os05t0228400-01 BGIOSGA018993-TA BGIOSGA018542-TA 926 +
Os05t0229475-00 Os05t0326625-00 BGIOSGA018488-TA BGIOSGA018294-TA 398 +
Os05t0330700-02 Os05t0597700-01 BGIOSGA018291-TA BGIOSGA017428-TA 1924 +
Os06t0101000-01 Os06t0196900-02 BGIOSGA022119-TA BGIOSGA022469-TA 813 +
Os06t0198500-00 Os06t0731700-01 BGIOSGA021720-TA BGIOSGA020493-TA 2579 +
Os07t0100200-01 Os07t0695400-01 BGIOSGA024990-TA BGIOSGA023660-TA 3055 +
Os08t0100150-01 Os08t0567200-01 BGIOSGA027824-TA BGIOSGA026457-TA 2898 +
Os09t0101100-01 Os09t0287500-01 BGIOSGA030257-TA BGIOSGA030063-TA 410 +
Os09t0293400-01 Os09t0573200-01 BGIOSGA030459-TA BGIOSGA031320-TA 1853 +
还有很多绘图样式，参考
https://github.com/tanghaibao/jcvi/wiki/MCscan-(Python-version)
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