主页 / unix / 问题 / 755262
Accepted
Paulo Sergio Schlogl
Asked: 2023-08-30 01:50:01 +0800 CST

建议使用安全命令在脚本使用文件后删除文件

  • 772

我有这个脚本，我想在其中添加一行，在串联后，安全地删除 *.dump 文件，因为它们很大，而且我没有空间用于串联文件和转储文件。jelly 是一个 txt 文件，其中包含一行一行的基因组 ID 列表，如下所示：

GCA....
GCA....and so on.

我有一堆转储文件名，以基因组 id 命名，有两列：例如。GCA...1.dump 就像：

A 57575757
C 6656565..

前任。GCA...2.dump 就像：

AA 6565656
AT 6565656...

所以我有每个基因组 ID 的 14 个转储文件（1-14 ngrams）。因此，我想为每个基因组 ID 连接所有 1-14，然后删除基于 jelly 文件的使用过的转储文件。最后，我只需要在创建的新目录中有一个名为 *.counts 的文件。

#! usr/bin/env bash

dir_in=$1 # Jelly_count
super=$2 # Archaea/Bacteria
group=$3 # Asgard_group/Pseudomonadota
sub=$4 # Aquificota
dir_out=Counts/"${super}"/"${group}"/"${sub}"/CHR

if [ ! -d "${dir_out}" ]; then
  mkdir -p "${dir_out}"
fi
# read the ids in jelly file
for id in $(cat "${dir_in}"/"${super}"/"${group}"/"${sub}"/jelly);
do
  echo "Concatenating files from genome ${id}"
  # make a loop from 1 to 14 or any other range I need
  for i in $(seq $5 $6);
    do
      # concatenate all 14 tsv files in one
      csvtk concat "${dir_in}"/"${super}"/"${group}"/"${sub}"/CHR/"${id}"_"${i}".dump >> "${dir_out}"/"${id}"_chr_kmer.counts
     # then delete all the 14 dump files
     # MAYBE ?????
     **find "${dir_in}"/"${super}"/"${group}"/"${sub}". -name '*.dump' -delete**
    done
    
done

我尝试过rm，但还有更好的方法吗？

谢谢你们。

保罗

rm

1 个回答

  1. Best Answer

    我猜原来的应该是这样运行的

     myscript   Jelly_count  Archaea/Bacteria Asgard_group/Pseudomonadota Aquificota 1 14

    可能首选项是 cat "$ff" >> "$F" && rm "$ff"我首先设置ff为文件名的位置。

    我会尝试以下方法。我希望那里没有太多/任何拼写错误。

    #!/bin/bash
#This file is named   script1

set -e    # exit on most errors. (This may be safer.)

dir_in="$1"    # Jelly_count
super="$2"     # Archaea/Bacteria
group="$3"     # Asgard_group/Pseudomonadota
sub="$4"      # Aquificota

#   $5  $6     means take counts from $5 to $6

dir_out=Counts/"${super}"/"${group}"/"${sub}"/CHR

if [ ! -d "${dir_out}" ]; then
  mkdir -p "${dir_out}"
fi
# read the ids in jelly file
for id in $(cat "${dir_in}"/"${super}"/"${group}"/"${sub}"/jelly);
do
  echo "Concatenating files from genome ${id}"
  # make a loop from 1 to 14 or any other range I need
  F="${dir_out}"/"${id}"_chr_kmer.counts
  if [ -e "$F" ]; then
       echo "File $F already exists, I do not like that";
       # exit; # the safest
       echo "<ENTER> to skip this and continue; <Ctrl-C> to stop";
       read
       # # An alternative: leave the file be and `continue`
       continue
       # # An alternative:
       # mv "$F" "$F"-old-"$(date)"-$$
       # # Alternative2 : just print warning:
       # echo "File $F already exists, we will make it even bigger!"
       # # Alternative3 : delete file
       # echo "File $F already exists, I am deleting it now."
       # rm "$F"
  fi
  for i in $(seq $5 $6);
    do
      ff="${dir_in}"/"${super}"/"${group}"/"${sub}"/CHR/"${id}"_"${i}".dump
      echo -n "about to delete: "
      wc -l "$ff"  # Print number of lines
      # cat and remove
      cat "$ff" >> "$F" && rm "$ff"
    done
    echo -n "The new file   : "
    wc -l "$F"  # Print number of lines

    echo "<ENTER> to proceed with the next; <Ctrl-C> to stop";
    read

done

    这将再次运行，就像

     script1   Jelly_count  Archaea/Bacteria Asgard_group/Pseudomonadota Aquificota 1 14

    （稍后可以去掉echo -n和wc行，行加上echo+ read。这里的wc意思是字数，wc -l实际上是行数。）

    • 1

相关问题