Question

我有几个.pdb文件需要处理才能从中检索现成的值。我已经制作了一个bash脚本来尝试将所有命令组合在一起。

我对这个脚本的具体问题是两个：

我尝试在Ubuntu的命令行上通过键入/输入./myscript.bash在bash中运行它并且它没有将所需文件输出到该文件夹时，我的脚本冻结了。我的脚本中可能导致冻结的错误是什么？

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

我不知道如何用bash编写这个命令。您在开头看到的grep会将包含任何model *文本的行打印到名为$ file ___。txt的文件中。我需要以特定格式使用它，我将其包含在grep下面的＃＆＃39; 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的使用是否正确？

以下是完整的参考脚本：

#! /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

我认为你的脚本是冻结的，因为所有变量都是空的，而grep之类的命令在STDIN上被阻塞了！我很快清理了你的脚本，并添加了一些我认为你可能需要的代码（前缀为＆＃34; GLR＆＃34;注释）。研究这个，它应该让你更接近。

#!/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

bash脚本冻结了

1 个答案: