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Bash中的矩阵运算

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Bash中的矩阵运算

重点是我需要转置一个大文件 - 1600 乘以 80k，但条目不是制表符分隔的，而只是 U 和 K，所以看起来像

UUUUTTTUTUTUUUTUTUT
TTUTUTUTUUTUTUTUTUT

在 bash、python 或 perl 中有没有最好的方法可以做到这一点？

答案1

下面将使用接近零的内存资源转置具有任意行数和列数的矩阵。

#!/bin/sh
for i in $(seq 1 $(head -n1 "$1" | wc -c)); do 
    awk -v c=$i 'BEGIN{FS=""}{printf $c}' "$1"
    echo
done

用一个有意义的名字保存它（例如transpose.sh），使其可执行（chmod +x transpose.sh）并像这样使用它：

./transpose.sh matrix.txt

输出：

UT
UT
UU
UT
TU
TT
TU
UT
TU
UU
TT
UU
UT
UU
TT
UU
TT
UU
TT

怎么运行的：

  • $(head -n1 "$1" | wc -c)：计算列数
  • for i in $(seq 1 $num_cols); do ... done：对每一列运行此循环
  • awk -v c=$i 'BEGIN{FS=""}{printf $c}' "$1"：解析矩阵文件。当前列号（来自父循环的当前迭代）保存在awk变量中c。使用它来按顺序打印此列的所有值（$c）（无换行符 - 使用printf）

答案2

两个想法：

  1. perl

    perl -ne '
        chomp; 
        $l = length if $. == 1; 
        push @rows, [split //];
    } END {
        for ($i=0; $i<$l; $i++) {
            for ($j=0; $j<$.; $j++) {
                print $rows[$j][$i];
            } 
            print "\n";
        }
' file

  2. ruby 有一个方便的Array.transpose方法

    ruby -e 'puts IO.readlines(ARGV.shift)
                .map {|line| line.chomp.split("")}
                .transpose
                .map {|row| row.join("")}
                .join("\n")
' file

嗯，这些会占用大量内存。另一种实现

  1. perl

    perl -ne '
        chomp; 
        if ($. == 1) {
            @data = split //;
        } else {
            @chars = split //; 
            $data[$_] .= $chars[$_] for 0..$#chars;
        }
    } END {
        print join("\n", @data), "\n";
' file

  2. 红宝石

    ruby -e '
  file = File.open(ARGV.shift)
  data = file.gets.chomp.split("")
  file.each do |line| 
    line.chomp.split("").each_with_index do |char, idx| 
      data[idx] << char
    end
  end
  puts data.join("\n")
' file

我就是不能放过这件事 ;)

基准测试

               1 MB file         10 MB file           100 MB file
-----------------------------------------------------------------
         |   time  memory  |    time   memory  |     time  memory
perl v1  |  0.54s  85800k  |   4.59s  815140k  |        -       -
perl v2  |  0.47s   6776k  |   4.29s   22204k  |   41.88s 180404k
ruby v1  |  1.19s 137960k  |  14.63s  961736k  |        -       -
ruby v2  |  1.04s  12296k  |   9.75s   27816k  |  101.75s 185908k
gawk     |  1.15s 233056k  |  12.37s 2291404k  |        -       -
choroba  |  0.45s  76740k  |   3.90s  728888k  |        -       -

Choroba 的 perl 在时间竞赛中获胜，但我的第二次实现在内存方面遥遥领先。

文字记录：

$ yes 123456789 | head -n 100000 > big
$ yes 123456789 | head -n 1000000 > bigger
$ yes 123456789 | head -n 10000000 > biggest
$ ls -l big*
-rw-r--r-- 1 jackman jackman   1000000 Jun 24 14:33 big
-rw-r--r-- 1 jackman jackman  10000000 Jun 24 14:33 bigger
-rw-r--r-- 1 jackman jackman 100000000 Jun 24 14:33 biggest
$ time perl -n transpose_v1.pl big >/dev/null
0.54user 0.05system 0:00.98elapsed 61%CPU (0avgtext+0avgdata 85800maxresident)k
3080inputs+0outputs (15major+20501minor)pagefaults 0swaps
$ time perl -n transpose_v1.pl bigger >/dev/null
4.59user 0.39system 0:04.98elapsed 99%CPU (0avgtext+0avgdata 815140maxresident)k
0inputs+0outputs (0major+202823minor)pagefaults 0swaps
$ time perl -n transpose_v2.pl big >/dev/null
0.47user 0.00system 0:00.48elapsed 99%CPU (0avgtext+0avgdata 6776maxresident)k
0inputs+0outputs (0major+819minor)pagefaults 0swaps
$ time perl -n transpose_v2.pl bigger >/dev/null
4.29user 0.01system 0:04.31elapsed 99%CPU (0avgtext+0avgdata 22204maxresident)k
0inputs+0outputs (0major+5042minor)pagefaults 0swaps
$ time perl -n transpose_v2.pl biggest >/dev/null
41.88user 0.11system 0:42.01elapsed 99%CPU (0avgtext+0avgdata 180404maxresident)k
0inputs+0outputs (0major+44590minor)pagefaults 0swaps
$ time ruby transpose_v1.rb  big >/dev/null
1.19user 0.10system 0:01.58elapsed 81%CPU (0avgtext+0avgdata 137960maxresident)k
5856inputs+0outputs (23major+33375minor)pagefaults 0swaps
$ time ruby transpose_v1.rb  bigger >/dev/null
14.63user 0.48system 0:15.12elapsed 99%CPU (0avgtext+0avgdata 961736maxresident)k
0inputs+0outputs (0major+239378minor)pagefaults 0swaps
$ time ruby transpose_v2.rb  big >/dev/null
1.04user 0.02system 0:01.07elapsed 98%CPU (0avgtext+0avgdata 12296maxresident)k
0inputs+0outputs (0major+2020minor)pagefaults 0swaps
$ time ruby transpose_v2.rb  bigger >/dev/null
9.75user 0.02system 0:09.79elapsed 99%CPU (0avgtext+0avgdata 27816maxresident)k
0inputs+0outputs (0major+6051minor)pagefaults 0swaps
$ time ruby transpose_v2.rb  biggest >/dev/null
101.75user 0.21system 1:41.99elapsed 99%CPU (0avgtext+0avgdata 185908maxresident)k
0inputs+0outputs (0major+45600minor)pagefaults 0swaps
$ time gawk -f transpose.gawk big >/dev/null
1.15user 0.12system 0:01.28elapsed 99%CPU (0avgtext+0avgdata 233056maxresident)k
0inputs+0outputs (0major+58542minor)pagefaults 0swaps
$ time gawk -f transpose.gawk bigger >/dev/null
12.37user 1.03system 0:13.40elapsed 99%CPU (0avgtext+0avgdata 2291404maxresident)k
0inputs+0outputs (0major+580302minor)pagefaults 0swaps
$ time perl transpose_choroba.pl  big >/dev/null
0.45user 0.04system 0:00.58elapsed 84%CPU (0avgtext+0avgdata 76740maxresident)k
112inputs+0outputs (1major+18282minor)pagefaults 0swaps
$ time perl transpose_choroba.pl  bigger >/dev/null
3.90user 0.37system 0:04.28elapsed 99%CPU (0avgtext+0avgdata 728888maxresident)k
0inputs+0outputs (0major+181291minor)pagefaults 0swaps

答案3

Perl 解决方案：

#!/usr/bin/perl
use strict;
use warnings;

my @arr;
while (my $line = <>) {              # Read the input line by line.
    chomp $line;                     # Remove a newline.

    # Distribute the characters to subarrays of the array:
    push @{ $arr[$_] }, substr $line, $_, 1
        for 0 .. length($line) - 1;
}
print @$_, "\n" for @arr;

不过，您需要大量内存来转置大型矩阵。

答案4

使用gawk

sudo apt-get install gawk

创建 awk 脚本transpose

BEGIN { FS = "" }
{
    for (i=1; i<=NF; i++) {
        a[NR,i] = $i
    }
}
NF>p { p = NF }
END {
    for(j=1; j<=p; j++) {
        str=a[1,j]
        for(i=2; i<=NR; i++){
            str=str""a[i,j];
        }
        print str
    }
}

并开始

gawk -f transpose <your_input_file> > <your_output_file>

例子

% cat foo
UUUUTTTUTUTUUUTUTUT
TTUTUTUTUUTUTUTUTUT

% gawk -f transpose foo
UT
UT
UU
UT
TU
TT
TU
UT
TU
UU
TT
UU
UT
UU
TT
UU
TT
UU
TT

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