bash 스크립트가 작동하지 않습니다.

Question

쉽게 사용할 수있는 값을 검색하기 위해 처리해야하는 .pdb 파일이 여러 개 있습니다. 나는 bash 스크립트를 만들어서 모든 명령을 하나로 묶어 보았다. 이 스크립트에 대한

내 구체적인 질문은 두 가지이다 : 나는/입력 ./myscript.bash를 입력하여 우분투에서 명령 줄에서 bash는 그것을 실행하려고하고 후

1. 내 스크립트가 동결 원하는 파일을 폴더로 출력하지 않습니다. 이 스크립트가 멈추는 원인이 될 수있는 실수는 무엇입니까? 마지막 명령에서

2. ,

   grep 'model*' $file >> $file"-confscore".txt 
   #command to keep only the 1-5 lines from each dir I want to keep that contain this full format " model1 -5.00 0.21+-0.05 19.9+-1.8  404  0.003 " then >> combinedcscore.txt 
   #Then reformat it to just "$dir model1 -5.00" >> newcombcscore.txt  
   

   나는 bash는이 명령을 작성하는 방법을 모르겠어요. 처음에 볼 수있는 grep은 모든 모델 * 텍스트를 포함하는 행을 $ file ___. txt라는 파일에 인쇄합니다. grep 밑의 # 라인에 포함 된 특정 형식으로이 파일이 필요합니다. 다음을 사용하려고합니다 :

   for files in $dirs; do 
   awk -F':' ' { print $dir model* firstvalueidk? }' >> newcombcscore.txt 
   

   awk를 올바르게 사용하고 있습니까?

여기 참조를 위해 전체 스크립트입니다 :

#! /usr/bin/env bash 

#Step 0 - Set up variables & navigate to app. directory 
set GETLOCATION = "~/Desktop/DCompartment/RolandoHT_Scripts/Perl_Scripts" 
set GETNAME = "get_right_pdb_format.pl" 
set SSLOCATION = "~/Desktop/DCompartment/RolandoHT_Scripts/Perl_Scripts" 
set SSNAME = "get_ss_dssp_itasser.pl" 
set PROTALOCATION = "~/Desktop/protAlign-master/" 
set dirs = ~/Videos/Proteins/* 


#Step 1 - Process PDB for readily available values 

for dir in $dirs; do 
rm `cscore|model*.pdb|seq.fasta` 
done 

for dir in $dirs; do 
for file in *.pdb; do 
perl $GETLOCATION/$GETNAME $file 
dssp -i $file"-fix" -o $file.dssp 
perl $SSLOCATION/$SSNAME $file.dssp $file"-out" 
done 

for file in $dirs/*.dssp; do 
grep 'ACCESSIBLE SURFACE OF PROTEIN' $file >> $file"-SASA".txt 
done 

for file in $dirs/*.txt; do 
echo "$file `cat $file`" >> $dir-combinedSASAs.txt 
done 
done 
#Step 2 - Set up tool 
for dir in $dirs; do 
./$PROTALOCATION/initialize.sh 
source $PROTALOCATION/bin/activate 
done 
#Step 3 - Start analyzing files 
for dir in $dirs; do 
for file in *.pdb; do 
./$PROTALOCATION/program_name.py $dir $dir/native.pdb $dir-SPAR 
done 
done 
for file in $dirs/data; do 
set filerep = native-*.txt 
grep 'TM-score' $filerep >> combinedreports.txt 
awk 'FNR%2' combinedreports.txt > newcombinedrep.txt 
done 

for dir in $dirs; do 
for file in cscore; do 
grep 'model*' $file >> $file"-confscore".txt 
#command to keep only the 1-5 lines from each dir I want to keep that contain this full format " model1 -5.00 0.21+-0.05 19.9+-1.8  404  0.003 " then >> combinedcscore.txt 
#Then reformat it to just "$dir model1 -5.00" >> newcombcscore.txt  
done 
done 

Answer 1

나는 모든 변수가 비어 있고 grep 같은 명령은 STDIN에 차단하기 때문에 스크립트가 동결 생각! 나는 신속하게 스크립트를 정리하고 내가 필요하다고 생각하는 코드 (GLR 접두어가 붙은 코드)를 추가했다. 이것을 공부하면 훨씬 더 가까워 질 것입니다.

#!/bin/bash 

# Step 0 - Set up variables & navigate to app. directory 
GETLOCATION=~/Desktop/DCompartment/RolandoHT_Scripts/Perl_Scripts 
GETNAME=get_right_pdb_format.pl 
SSLOCATION=~/Desktop/DCompartment/RolandoHT_Scripts/Perl_Scripts 
SSNAME=get_ss_dssp_itasser.pl 
PROTALOCATION=~/Desktop/protAlign-master 
dirs=~/Videos/Proteins/* 


# GLR: uncomment the next line for debugging 
#set -x 


#Step 1 - Process PDB for readily available values 

for dir in $dirs; do 
    # GLR: Assume you want to change directory here? 
    pushd $dir 

    rm `cscore|model*.pdb|seq.fasta` 

    # GLR: back to original directory 
    popd 
done 


for dir in $dirs; do 
    # GLR: Assume you want to change directory here? 
    pushd $dir 

    for file in *.pdb; do 
     perl $GETLOCATION/$GETNAME $file 
     dssp -i ${file}-fix -o $file.dssp 
     perl $SSLOCATION/$SSNAME $file.dssp ${file}-out 
    done 

    for file in $dirs/*.dssp; do 
     grep 'ACCESSIBLE SURFACE OF PROTEIN' $file >> ${file}-SASA.txt 
    done 

    for file in $dirs/*.txt; do 
     echo "$file `cat $file`" >> $dir-combinedSASAs.txt 
    done 

    # GLR: back to original directory 
    popd 
done 


#Step 2 - Set up tool 
for dir in $dirs; do 
    # GLR: Assume you want to change directory here? 
    pushd $dir 

    ./$PROTALOCATION/initialize.sh 
    . $PROTALOCATION/bin/activate 

    # GLR: back to original directory 
    popd 
done 


#Step 3 - Start analyzing files 
for dir in $dirs; do 
    # GLR: Assume you want to change directory here? 
    pushd $dir 

    for file in *.pdb; do 
     ./$PROTALOCATION/program_name.py $dir $dir/native.pdb $dir-SPAR 
    done 

    # GLR: back to original directory 
    popd 
done 

# GLR: this won't do what you want 
#for file in $dirs/data; do 

for dir in $dirs; do 
    # GLR: Assume you want to change directory here? 
    pushd $dir/data 

    #;filerep=native-*.txt 
    #;grep 'TM-score' $filerep >> combinedreports.txt 

    grep 'TM-score' native-*.txt >> combinedreports.txt 
    awk 'FNR%2' combinedreports.txt > newcombinedrep.txt 

    # GLR: back to original directory 
    popd 
done 

for dir in $dirs; do 
    # GLR: Assume you want to change directory here? 
    pushd $dir 

    for file in cscore; do 
     grep 'model*' $file >> ${file}-confscore.txt 

     # command to keep only the 1-5 lines from each dir I want to keep 
     # that contain this full format 
     # " model1 -5.00 0.21+-0.05 19.9+-1.8  404  0.003 " 
     # then >> combinedcscore.txt 

     # Then reformat it to just "$dir model1 -5.00" >> newcombcscore.txt  
    done 

    # GLR: back to original directory 
    popd 
done 


exit 0