Shell_Sh_Code_Example

#这个是Shell脚本，不是Python命令行文件

#!/bin/sh
# Run scripts with Python (and modpy.sh if needed) if possible, rather
# than the modXXX script (which only works correctly if Python 2.3 is installed)
modpy="../../bin/modpy.sh"
# If modpy.sh doesn't exist, assume we have Python set up correctly already
# (e.g. Mac or RPM install, or PYTHONPATH and LD_LIBRARY_PATH set):
if test "${PYTHON}x" != "x"; then
  pyint="${PYTHON}"
else
  pyint="python"
fi
if test ! -f ${modpy}; then
  modpy="${pyint}"
else
  modpy="${modpy} ${pyint}"
fi
# Only use Modeller through Python if 1) an import succeeds, 2) the 'modeller'
# module imported is really Modeller (not a spurious modeller.py in the path
# somewhere) and 3) the version matches that these examples were built with
run_version=`${modpy} - 2>/dev/null <<END
import sys
from modeller import *
v = info.version_info
if isinstance(v, tuple):
    v = ".".join([str(i) for i in v])
sys.stdout.write(v + '\n')
END
`
build_version="9.11"

#-- Rewrite By JunH
workPath="../ModellerWorkFolder/TvLDH"
PDBID="TvLDH"
PYFULLPATH="/home/protein/JunHWorkSpace/SimpleModeller"

if [ $# != 2 ]
then
  echo "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!"
  echo "!!         输入参数不正确         !!"
  echo "!!      导出失败，未生成文件      !!"
  echo "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!"
  exit 1
fi

workPath=$1
PDBID=$2

# run_script build_profile
if test "${run_version}" = "${build_version}"; then
  cmd="${modpy} $PYFULLPATH/build_profile.py $PYFULLPATH $workPath $PDBID.ali > $workPath/temp/build_profile.log"
else
  cmd="mod9.11 $PYFULLPATH/build_profile.py"
fi
echo "$cmd"
# 运行Cmd
eval "$cmd"

# translate workPath + '/temp/build_profile.prf' File
# 去除文件$workPath/temp/build_profile.prf的第1-7行后保存在$workPath/temp/build_profile.prf.copy
sed '1,7d' $workPath/temp/build_profile.prf > $workPath/temp/build_profile.prf.copy

# 选取文件$workPath/temp/build_profile.prf.copy中第12个域值中最小的值
minilize=`awk 'BEGIN { a = 1 } { if ($12 < a) a = $12; } END { print a }' $workPath/temp/build_profile.prf.copy`
# 选取文件$workPath/temp/build_profile.prf.copy中所有最小的值
ProteinPDBIDList=`awk '{ if ($12 == '$minilize') print $2 }' $workPath/temp/build_profile.prf.copy`

# format ProteinPDBIDList
# 将$ProteinPDBIDList中所有的"  "变成" "
pPDBIDList=`echo $ProteinPDBIDList | sed 's/ / /g'`

#run_script compare
if test "${run_version}" = "${build_version}"; then
  cmd="${modpy} $PYFULLPATH/compare.py $PYFULLPATH $workPath $pPDBIDList > $workPath/temp/compare.log"
else
  cmd="mod9.11 $PYFULLPATH/compare.py"
fi
echo "$cmd"
eval "$cmd"

# translate workPath + '/temp/family.mat' File
# remove the first count line
sed '1,1d' $workPath/temp/family.mat > $workPath/temp/family.mat.copy

# search minilize score
minScore=1000
# while循环读取$workPath/temp/family.mat.copy每一行
while read line
do
  # 将line用" "分割后选取第2个域给atScore
   atScore=`echo $line | cut -d" " -f2`
   # 将atScore的第2个到最后一个字符截取后赋给score
   score=`echo $atScore | cut -c2-`
   # 比较score中的数值是否比minScore中的小如果是叫将socre赋给minScore
   if (echo ${score} ${minScore} | awk '!($1<$2){exit 1}') then
        tpdbID=`echo $line | cut -d" " -f1`
 minScore=$score
   fi
done < $workPath/temp/family.mat.copy

# 将tpdbID的第1个到第4个字符截取后赋给pdbCode
pdbCode=`echo $tpdbID | cut -c-4`
# 将tpdbID的第5个到最后一个字符截取后赋给pdbChain
pdbChain=`echo $tpdbID | cut -c5-`

#run_script align2d
if test "${run_version}" = "${build_version}"; then
  cmd="${modpy} $PYFULLPATH/align2d.py $PYFULLPATH $workPath $PDBID $pdbCode $pdbChain > $workPath/temp/align2d.log"
else
  cmd="mod9.11 $PYFULLPATH/align2d.py"
fi
echo "$cmd"
eval "$cmd"

#run_script model-single
if test "${run_version}" = "${build_version}"; then
  cmd="${modpy} $PYFULLPATH/model-single.py $workPath $PDBID $tpdbID > $workPath/temp/model-single.log"
else
  cmd="mod9.11 $PYFULLPATH/model-single.py"
fi
echo "$cmd"
eval "$cmd"

mv "$PDBID.B99990001.pdb" "$workPath/$PDBID.pdb"
rm -f $PDBID*