一、run_DELPHI.sh文件的理解
#!/bin/bash
#set -x
# This is the DELPHI program entrance
# Usage: ./run_DELPHI.sh [INPUT_FN]
which python #查看python解释器的路径
export INPUT_FN=$1
## 添加当前位置到动态库环境变量,export的作用表示新增一个INPUT_FN的环境变量,INPUT_FN这个变量表示输入蛋白质的序列,$1表示执行脚本的第一个参数。
# OUT_DIR=${PRO_DIR}/tmp_human_pssm_last1000
# export TMP_DIR=${PRO_DIR}/tmp-$(date +%Y-%m-%d-%H-%M-%S)
# export TMP_DIR=${PRO_DIR}/tmp_human_pssm_last1000
echo "PRO_DIR: $PRO_DIR" #echo类似于打印的意思,表示字符串的输出。输出变量PRO_DIR和TMP_DIR
echo "TMP_DIR: $TMP_DIR"
#####################
#check PSSM database#
#####################
# argv[2]: PSSM_DIR=${TMP_DIR}/PSSM_raw/1/
echo "load_PSSM_DB"
python3 utils/load_PSSM_DB.py ${INPUT_FN} ${TMP_DIR}/PSSM_raw/1
#运行utils文件中load_PSSM_DB.py的python文件,变量有INPUT_FN、TMP_DIR、PSSM_raw执行这几个变量的第一个参数
####################
# compute features#
####################
bash feature_computation/compute_features.sh $INPUT_FN
#执行feature_computation文件夹下面的compute_features.sh文件,INPUT_FN为变量。
# ####################
# # run DELPHI #
# ####################
python3 predict.py -i $INPUT_FN -d $TMP_DIR -o $OUT_DIR -c 1
#进行预测
if [ $? -ne 0 ]
then
echo "[Error:] DELPHI returns 1!"
fi
以上代码的流程图
二、compute_features.sh文件的理解
通过以下的sh文件对12个特征进行计算。
#!/bin/bash
#set -x
mkdir -p $TMP_DIR
#创建TMP_DIR的文件夹
# ####################
# ## ECO ##
# #################### (verified)
echo "computing ECO"
${PRO_DIR}/feature_computation/ECO/run_ECO.sh
# ####################
# ## RSA ##
# #################### (verified)
echo "computing RSA"
${PRO_DIR}/feature_computation/RSA/run_RSA.sh &
# ####################
# ## RAA ##
# #################### (verified)
echo "computing RAA"
${PRO_DIR}/feature_computation/RAA/run_RAA.sh &
# ####################
# ## HYD ##
# #################### (verified)
echo "computing HYD"
${PRO_DIR}/feature_computation/HYD/run_HYD.sh &
# ####################
# ## PKA ##
# #################### (verified)
echo "computing PKA"
${PRO_DIR}/feature_computation/PKA/run_PKA.sh &
# ####################
# ## POSITION ##
# #################### (verified)
echo "computing POSITION"
${PRO_DIR}/feature_computation/POSITION/run_POSITION.sh &
# ####################
# ## PHY_Char ##
# #################### (verified)
echo "computing PHY_Char"
${PRO_DIR}/feature_computation/PHY_Char/run_PHY_Char.sh &
# ####################
# ## PHY_Prop ##
# #################### (verified)
echo "computing PHY_Prop"
${PRO_DIR}/feature_computation/PHY_Prop/run_PHY_Prop.sh &
# ####################
# ## Pro2Vec_1D ##
# #################### (verified)
echo "computing Pro2Vec_1D"
${PRO_DIR}/feature_computation/Pro2Vec_1D/run_Pro2Vec_1D.sh &
# ####################
# ## Anchor ##
# #################### (verified)
echo "computing Anchor"
${PRO_DIR}/feature_computation/Anchor/run_Anchor.sh &
# ####################
# ## HSP ##
# #################### (verified)
echo "computing HSP"
${PRO_DIR}/feature_computation/HSP/run_HSP.sh
####################
## PSSM ##
####################
echo "computing PSSM"
${PRO_DIR}/feature_computation/PSSM/run_PSSM.sh