linux - bash 脚本卡住

Question

我有几个 .pdb 文件需要处理，以便从中检索现成可用的值。我制作了一个 bash 脚本来尝试将所有命令组合在一起。

我关于这个脚本的具体问题有两个:

1. 我尝试通过键入/输入 ./myscript.bash 在 Ubuntu 命令行上的 bash 中运行脚本后，我的脚本卡住了，并且它没有将所需的文件输出到文件夹。我的脚本中有什么错误可能导致此卡住？

2. 在最后的命令中，

   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    
   

   我不知道如何在 bash 中编写此命令。您在开头看到的 grep 会将包含任何模型*文本的行打印到名为 $file___.txt 的文件中。我需要特定格式的文件，我将其包含在 grep 下面的 #'d 行中。我正在考虑使用:

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

   我对 awk 的使用正确吗？

完整脚本供引用:

#! /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

我认为您的脚本正在卡住，因为您的所有变量都是空的，并且 grep 之类的命令在 STDIN 上阻塞!我快速清理了您的脚本并添加了一些我认为您可能需要的代码(以“GLR”注释为前缀)。研究这个，它应该会让你更接近。

#!/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