OrthoDB / Orthologer

Orthologer 为 OrthoDB 的应用程序

1. 安装

用docker安装Orthologer :
docker pull ezlabgva/orthologer:v2.3

Orthologer所在的URL为 :
https://hub.docker.com/r/ezlabgva/orthologer

报错：

• 1. Error response from daemon: manifest for ezlabgva/orthologer:latest not found: manifest unknown: manifest unknown
• 解决：https://blog.csdn.net/qq_20042935/article/details/105043400

2. 建立Orthologer的工作环境

(base) zhiyong@zhiyong-OptiPlex-7050:~/Application/test/Sequences$ id -u   '#查看当前用户的UID
1000  #当前用户的UID为1000
(base) zhiyong@zhiyong-OptiPlex-7050:~/Application/test/Sequences$ mkdir Orthologer_env  #创建Orthologer的工作目录
(base) zhiyong@zhiyong-OptiPlex-7050:~/Application/test/Sequences$ cd Orthologer_env/
(base) zhiyong@zhiyong-OptiPlex-7050:~/Application/test/Sequences/Orthologer_env$ pwd
/home/zhiyong/Application/test/Sequences/Orthologer_env
(base) zhiyong@zhiyong-OptiPlex-7050:~/Application/test/Sequences/Orthologer_env$ sudo docker run -u 1000 -v /home/zhiyong/Application/test/Sequences/Orthologer_env:/odbwork ezlabgva/orthologer:v2.3 setup_odb.sh  #在当前目录下创建Orthologer的工作环境

工作环境创建成功后，目录中的内容如下

(base) zhiyong@zhiyong-OptiPlex-7050:~/Application/test$ ll
总用量 84
drwxrwxr-x 12 zhiyong zhiyong  4096 3月  29 19:32 ./
drwxrwxr-x  7 zhiyong zhiyong  4096 3月  29 19:31 ../
drwxr-xr-x  2 zhiyong root     4096 3月  29 19:31 bin/
drwxr-xr-x  2 zhiyong root     4096 3月  29 19:31 Cluster/
-rwxr-xr-x  1 zhiyong root    12846 3月  29 19:31 common.sh*
drwxr-xr-x  2 zhiyong root     4096 3月  29 19:31 docs/
drwxr-xr-x  6 zhiyong root     4096 3月  29 19:32 JobLog/
-rw-rw-r--  1 zhiyong zhiyong   124 3月  29 19:32 mydata.txt
-rwxr-xr-x  1 zhiyong root      880 3月  29 19:31 orthologer.sh*
drwxr-xr-x  6 zhiyong root     4096 3月  29 19:32 PWC/
drwxr-xr-x  2 zhiyong root     4096 3月  29 19:31 Rawdata/
drwxr-xr-x  2 zhiyong root     4096 3月  29 19:31 Results/
lrwxrwxrwx  1 zhiyong root       31 3月  29 19:31 sbin -> /usr/local/ORTHOLOGER-2.3.0/bin
drwxr-xr-x  2 zhiyong root     4096 3月  29 19:31 .scratch/
drwxr-xr-x  2 zhiyong root     4096 3月  29 19:46 Sequences/
-rw-r--r--  1 zhiyong root     1332 3月  29 19:31 setup.log
-rw-r--r--  1 zhiyong root      756 3月  29 19:31 .setup_project_uid1000.sh
-rwxr-xr-x  1 zhiyong root     1951 3月  29 19:31 setup_project_uid1000.sh*
drwxr-xr-x  2 zhiyong root     4096 3月  29 19:32 todo/

3. 将fasta文件转移至工作路径

• 1. fasta文件可以是DNA序列也可以是蛋白质序列
• 2. 在Orthologer的工作环境中创建新的目录(注意不要和原有目录重名)
• 3. 将用来做比较的fasta文件转移到此新目录下

4. 创建fasta文件引导文件

• 1. 在工作环境下创建此文件
• 2. 文件中包含物种标记(taxid)，以及对应fasta文件所在目录，具体格式如下：

(base) zhiyong@zhiyong-OptiPlex-7050:~/Application/OrthoDB_env$ cat mydata.txt  '#此文件是fasta文件引导文件
+Amel kkkk/Aeml_protein.fa  #第一列是物种标记(taxid)，注意前面加号"+"的添加(具体原因请查看帮助文件)；后面是对应fasta文件所在位置，其中kkkk是位于工作环境目录下的目录；两者之间用空格隔开
+Bimp kkkk/Bimp_protein.fa
+Bter kkkk/Bter_protein.fa
+Dmel kkkk/Dmel_protein.fa

note : 在写fasta文件目录的时候，只需要写fasta文件所在的这一层目录即可，否则报错

5. 将以上fasta引导文件中的fasta进行导入

sudo docker run -u 1000 -v /home/zhiyong/Application/test/Sequences/Orthologer_env:/odbwork ezlabgva/orthologer:v2.3 ./orthologer.sh manage -f mydata.txt

note : 此命令要在工作环境那层执行

6. 修改.todo文件

• 1. .todo 文件位于 todo 目录下，以 .todo 为拓展名
• 2. .todo 文件里包含将用于比对的物种标记(taxid)
• 3. .todo 文件的名字不重要，但拓展名非常重要

(base) zhiyong@zhiyong-OptiPlex-7050:~/Application/OrthoDB_env/todo$ cat Amel_Bter.todo  #这个文件将用于引导比较Amel和Bter
AMEL
BTER

(base) zhiyong@zhiyong-OptiPlex-7050:~/Application/OrthoDB_env/todo$ cat Amel_Bter_Dmel.todo  #这个文件将用于引导Amel，Bter和Dmel
AMEL
BTER
DMEL

7. 运行Orthologer container

sudo docker run -u 1000 -v /home/zhiyong/Application/test/Sequences/Orthologer_env:/odbwork ezlabgva/orthologer:v2.3  ./orthologer.sh -t todo/mydata.todo -r all

7.1 OrthoDB-pro-ID - gtf-translation-ID

• location: Rawdata/.fs.maptxt

(base) zhiyong@zhiyong-OptiPlex-7050:~/Application/OrthoDB_env/Rawdata$ cat ACER.fs.maptxt|head

ACER:000000 NP_001315405.1 icarapin-like precursor [Apis cerana]
ACER:000001 NP_001315406.1 odorant receptor coreceptor [Apis cerana]
ACER:000002 NP_001315407.1 odorant receptor 30a-like [Apis cerana]
ACER:000003 NP_001315409.1 major royal jelly protein 5 precursor [Apis cerana]
ACER:000004 NP_001315410.1 period circadian protein [Apis cerana]
ACER:000005 NP_001315411.1 opsin, ultraviolet-sensitive [Apis cerana]
ACER:000006 NP_001315412.1 opsin, blue-sensitive [Apis cerana]
ACER:000007 NP_001315413.1 vitellogenin precursor [Apis cerana]
ACER:000008 NP_001315414.1 rhodopsin, long-wavelength [Apis cerana]
ACER:000009 NP_001315415.1 phosphoglycerate mutase 2 [Apis cerana]

• 第一列：OrthoDB-pro-ID
• 第二列：gtf-translation-ID

7.2 OG - gtf-translation-ID

• location: Results/mydata_orthogroups.txt

cat mydata_orthogroups.txt|head -20

0 XP_016906112.1 1 84 1 84 100 304.17 4.146e-63 
0 XP_016767410.1 1 84 1 84 100 304.17 4.146e-63 
1 XP_016910209.1 1 79 1 79 100 292.4 1.732e-56 
1 XP_006567534.1 1 79 1 79 100 292.4 1.732e-56 
2 XP_028519923.1 1 286 1 286 100 288.99 3.081e-215 
2 XP_006564532.1 1 286 1 286 100 288.99 3.081e-215 
3 XP_016908651.1 1 2874 1 2874 99.3 286.28 0 
3 XP_016908652.1 9 2874 1 2874 -1 100 0 
3 XP_003250904.2 1 2876 1 2876 99.3 286.28 0 
4 XP_016918707.1 1 232 1 232 99.5 285.78 1.028e-171 
4 NP_001165850.1 1 232 1 232 99.5 285.78 1.028e-171 
5 XP_016915986.1 1 336 1 336 100 285.25 8.206e-253 

• 第一列：OG
• 第二列：gtf-translation-ID