一、主頁

官網(wǎng)：https://effectors.csb.univie.ac.at/method/effectivet3
手冊：https://effectors.csb.univie.ac.at/sites/eff/files/others/TTSS_README.TXT
下載：https://effectors.csb.univie.ac.at/download

二、相關(guān)發(fā)布軟件

EffectiveT3 core software：TTSS_GUI-1.0.1.jar
EffectiveT3 classification module 1.0.1 (08/2009)：TTSS_STD-1.0.1.jar
EffectiveT3 classification module 2.0.2 (09/2015)：TTSS_STD-2.0.2.jar
EffectiveT3 classification module for human/animal-associated bacteria 1.0.1 (08/2009)：TTSS_ANIMAL-1.0.1.jar
EffectiveT3 classification module for plant-associated bacteria 1.0.1 (08/2009)：       TTSS_PLANT-1.0.1.jar
Training protein sequences for EffectiveT3 model 2.0.1 (positives)：TTSS_positive_training.faa
Training protein sequences for EffectiveT3 model 2.0.1 (negatives)：TTSS_negative_training.faa

三、核心軟件

Download the Effective classification modules:
TTSS_STD-2.0.1.jar     (based on all training data; 09/2015)
TTSS_STD-1.0.1.jar     (based on all training data; 08/2009)
TTSS_ANIMAL-1.0.1.jar  (based on training data from human/animal-associated bacteria; 08/2009)
TTSS_PLANT-1.0.1.jar   (based on training data from plant-associated bacteria; 08/2009)

四、使用方法

java -jar TTSS_GUI-latest.jar -f test.fasta -m TTSS_ANIMAL-1.0.1.jar -t selective -o test.out -q
or
java -jar TTSS_GUI-latest.jar -f test.fasta -m TTSS_STD-latest.jar -t cutoff=0.995 -o test.out -q

• 閾值：
  -t sensitive
  -t selective
  -t cutoff=0.995
  -m 預(yù)測module
  -f 輸入蛋白序列文件
  -o 輸出文件
  -q trigger command

五、conda安裝

github: https://bioconda.github.io/recipes/effectivet3/README.html

conda install effectivet3

• 使用

mkdir Result/t3ss
java -jar /home/cheng/huty/softwares/effectivet3/TTSS_GUI-1.0.1.jar \
-f Result/prokka/genome_prokka.faa \
-m /home/cheng/huty/softwares/effectivet3/TTSS_STD-1.0.1.jar \
-t cutoff=0.6 \
-o Result/t3ss/genome_t3ss.txt -q

java -jar TTSS_GUI-1.0.1.jar \
-f /home/cheng/huty/genome/Result/prokka/genome_prokka.faa \
-m TTSS_STD-2.0.2.jar \
-t selective \
-o test.txt -q

結(jié)果出錯了。。。