bash-用另一个文件中的一行替换文件中的多行
[英]bash - replacing multiple lines in a file with a single line from another file
问题描述
我到处搜索过，但仍然找不到所需的答案。 我有以下pdb文件（file1）：
ATOM 1 N SER A 1 31.848 -5.217 38.114 1.00 39.55
ATOM 2 CA SER A 1 31.668 -5.130 36.630 1.00 40.83
ATOM 3 C SER A 1 30.991 -3.833 36.183 1.00 40.24
ATOM 4 O SER A 1 30.868 -2.883 36.961 1.00 40.08
ATOM 5 CB SER A 1 30.854 -6.329 36.118 1.00 41.46
ATOM 6 OG SER A 1 31.600 -7.531 36.190 1.00 44.54
ATOM 7 N THR A 2 30.605 -3.796 34.906 1.00 39.92
ATOM 8 CA THR A 2 29.920 -2.658 34.286 1.00 38.97
ATOM 9 C THR A 2 28.542 -3.116 33.777 1.00 38.40
ATOM 10 O THR A 2 27.815 -2.341 33.141 1.00 38.79
ATOM 11 CB THR A 2 30.734 -2.067 33.086 1.00 39.67
ATOM 12 OG1 THR A 2 31.045 -3.101 32.139 1.00 38.83
ATOM 13 CG2 THR A 2 32.020 -1.403 33.566 1.00 38.83
使用gfortran（file2）进行一些计算后，我还有以下文件：
1 0.14364205034979632
2 0.50527753403393372
我想做的是只要文件1的第6列等于文件2的第1列，就用文件2的第2列替换文件1的第11列。 本质上，输出应该是这样的：
ATOM 1 N SER A 1 31.848 -5.217 38.114 1.00 0.14364205034979632
ATOM 2 CA SER A 1 31.668 -5.130 36.630 1.00 0.14364205034979632
ATOM 3 C SER A 1 30.991 -3.833 36.183 1.00 0.14364205034979632
ATOM 4 O SER A 1 30.868 -2.883 36.961 1.00 0.14364205034979632
ATOM 5 CB SER A 1 30.854 -6.329 36.118 1.00 0.14364205034979632
ATOM 6 OG SER A 1 31.600 -7.531 36.190 1.00 0.14364205034979632
ATOM 7 N THR A 2 30.605 -3.796 34.906 1.00 0.50527753403393372
ATOM 8 CA THR A 2 29.920 -2.658 34.286 1.00 0.50527753403393372
ATOM 9 C THR A 2 28.542 -3.116 33.777 1.00 0.50527753403393372
ATOM 10 O THR A 2 27.815 -2.341 33.141 1.00 0.50527753403393372
ATOM 11 CB THR A 2 30.734 -2.067 33.086 1.00 0.50527753403393372
ATOM 12 OG1 THR A 2 31.045 -3.101 32.139 1.00 0.50527753403393372
ATOM 13 CG2 THR A 2 32.020 -1.403 33.566 1.00 0.50527753403393372
我有以下代码：
gawk '
FNR==NR { pdb[NR]=$0; next }
{
split(pdb[FNR],flds,FS,seps)
while ( flds[6]==$1 ) {
flds[11]=$2
for (i=1;i in flds;i++)
printf "%s%s", flds[i], seps[i]
print ""
}
}
' "file1" "file2" > "output.pdb"
它完成了file1第一行的工作，并保持了间距的一致性。 问题在于它不会继续进行下一行，并且第一行也会永久重复。 有人能帮助我吗？
谢谢！ 我请你喝点啤酒:)
3 个解决方案
解决方案1
1 2016-07-17 10:44:16
我假设file1按第6列排序。
join -1 6 -2 1 file1 file2 -o 1.1,1.2,1.3,1.4,1.5,1.6,1.7,1.8,1.9,1.10,2.2 | column -t
输出：
ATOM 1 N SER A 1 31.848 -5.217 38.114 1.00 0.14364205034979632 ATOM 2 CA SER A 1 31.668 -5.130 36.630 1.00 0.14364205034979632 ATOM 3 C SER A 1 30.991 -3.833 36.183 1.00 0.14364205034979632 ATOM 4 O SER A 1 30.868 -2.883 36.961 1.00 0.14364205034979632 ATOM 5 CB SER A 1 30.854 -6.329 36.118 1.00 0.14364205034979632 ATOM 6 OG SER A 1 31.600 -7.531 36.190 1.00 0.14364205034979632 ATOM 7 N THR A 2 30.605 -3.796 34.906 1.00 0.50527753403393372 ATOM 8 CA THR A 2 29.920 -2.658 34.286 1.00 0.50527753403393372 ATOM 9 C THR A 2 28.542 -3.116 33.777 1.00 0.50527753403393372 ATOM 10 O THR A 2 27.815 -2.341 33.141 1.00 0.50527753403393372 ATOM 11 CB THR A 2 30.734 -2.067 33.086 1.00 0.50527753403393372 ATOM 12 OG1 THR A 2 31.045 -3.101 32.139 1.00 0.50527753403393372 ATOM 13 CG2 THR A 2 32.020 -1.403 33.566 1.00 0.50527753403393372
更新 ：
使用bash的printf：
printf "%s %6.d %-3s %s %s %s %s %s %s %s %s\n" $(join -1 6 -2 1 file1 file2 -o 1.1,1.2,1.3,1.4,1.5,1.6,1.7,1.8,1.9,1.10,2.2)
输出：
ATOM 1 N SER A 1 31.848 -5.217 38.114 1.00 0.14364205034979632 ATOM 2 CA SER A 1 31.668 -5.130 36.630 1.00 0.14364205034979632 ATOM 3 C SER A 1 30.991 -3.833 36.183 1.00 0.14364205034979632 ATOM 4 O SER A 1 30.868 -2.883 36.961 1.00 0.14364205034979632 ATOM 5 CB SER A 1 30.854 -6.329 36.118 1.00 0.14364205034979632 ATOM 6 OG SER A 1 31.600 -7.531 36.190 1.00 0.14364205034979632 ATOM 7 N THR A 2 30.605 -3.796 34.906 1.00 0.50527753403393372 ATOM 8 CA THR A 2 29.920 -2.658 34.286 1.00 0.50527753403393372 ATOM 9 C THR A 2 28.542 -3.116 33.777 1.00 0.50527753403393372 ATOM 10 O THR A 2 27.815 -2.341 33.141 1.00 0.50527753403393372 ATOM 11 CB THR A 2 30.734 -2.067 33.086 1.00 0.50527753403393372 ATOM 12 OG1 THR A 2 31.045 -3.101 32.139 1.00 0.50527753403393372 ATOM 13 CG2 THR A 2 32.020 -1.403 33.566 1.00 0.50527753403393372
解决方案2
1 已采纳 2016-07-17 14:31:14
这是一个非常普遍的问题，我很惊讶您找不到解决方案：
$ awk 'NR==FNR{a[$1]=$2;next} {$11=a[$6]} 1' file2 file1
ATOM 1 N SER A 1 31.848 -5.217 38.114 1.00 0.14364205034979632
ATOM 2 CA SER A 1 31.668 -5.130 36.630 1.00 0.14364205034979632
ATOM 3 C SER A 1 30.991 -3.833 36.183 1.00 0.14364205034979632
ATOM 4 O SER A 1 30.868 -2.883 36.961 1.00 0.14364205034979632
ATOM 5 CB SER A 1 30.854 -6.329 36.118 1.00 0.14364205034979632
ATOM 6 OG SER A 1 31.600 -7.531 36.190 1.00 0.14364205034979632
ATOM 7 N THR A 2 30.605 -3.796 34.906 1.00 0.50527753403393372
ATOM 8 CA THR A 2 29.920 -2.658 34.286 1.00 0.50527753403393372
ATOM 9 C THR A 2 28.542 -3.116 33.777 1.00 0.50527753403393372
ATOM 10 O THR A 2 27.815 -2.341 33.141 1.00 0.50527753403393372
ATOM 11 CB THR A 2 30.734 -2.067 33.086 1.00 0.50527753403393372
ATOM 12 OG1 THR A 2 31.045 -3.101 32.139 1.00 0.50527753403393372
ATOM 13 CG2 THR A 2 32.020 -1.403 33.566 1.00 0.50527753403393372
如果您关心保留空白：
$ awk 'NR==FNR{a[$1]=$2;next} {sub(/[^[:space:]]+[[:space:]]*$/,a[$6])} 1' file2 file1
ATOM 1 N SER A 1 31.848 -5.217 38.114 1.00 0.14364205034979632
ATOM 2 CA SER A 1 31.668 -5.130 36.630 1.00 0.14364205034979632
ATOM 3 C SER A 1 30.991 -3.833 36.183 1.00 0.14364205034979632
ATOM 4 O SER A 1 30.868 -2.883 36.961 1.00 0.14364205034979632
ATOM 5 CB SER A 1 30.854 -6.329 36.118 1.00 0.14364205034979632
ATOM 6 OG SER A 1 31.600 -7.531 36.190 1.00 0.14364205034979632
ATOM 7 N THR A 2 30.605 -3.796 34.906 1.00 0.50527753403393372
ATOM 8 CA THR A 2 29.920 -2.658 34.286 1.00 0.50527753403393372
ATOM 9 C THR A 2 28.542 -3.116 33.777 1.00 0.50527753403393372
ATOM 10 O THR A 2 27.815 -2.341 33.141 1.00 0.50527753403393372
ATOM 11 CB THR A 2 30.734 -2.067 33.086 1.00 0.50527753403393372
ATOM 12 OG1 THR A 2 31.045 -3.101 32.139 1.00 0.50527753403393372
ATOM 13 CG2 THR A 2 32.020 -1.403 33.566 1.00 0.50527753403393372
解决方案3
0 2016-07-17 14:13:49
此解决方案特定于gawk（请参阅按内容定义字段 ），并假定file2具有两列，并由单个空格分隔以根据要求获取输出
awk 'BEGIN {FPAT = "([[:space:]]*[[:alnum:][:punct:][:digit:]]+)"; OFS = "";} FNR==NR{a[$1]=$2; next} {$11=a[$6+0]} {print}' file2 file1
-
{$11=a[$6+0]}这样在数值上下文中而不是字符串比较中，像“ 1”和“ 2”这样的$6值将与像“ 1”和“ 2”这样的数组中a值匹配（感谢@Ed Morton为解释）
参考文献：
Bash：用另一组行替换文件中的多个连续行
[英]Bash: replacing multiple consecutive lines in a file with another set of lines
用bash中的另一个文件将一个文件中的第n行替换为下一行
[英]Replacing every nth line in one file with next line from another file in bash
Bash：如何将多行读入另一个文件，同时替换delim和在令牌$ n后截断
[英]Bash: how to read a multiple lines into another file, while replacing delims and truncating after token $n
从文件的开头和结尾的匹配模式中读取行，并将其附加到bash中的另一个文本文件中
[英]Read lines from a file enclosed matching pattern of starting line and ending line and append it to another text file in bash
Bash通过从另一个文件读取行号来从文本文件中获取行
[英]Bash get lines from text file by reading line numbers from another file
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