高效内存转置-AWK [英] Memory efficient transpose - Awk

问题描述

我正在尝试使用以下脚本来转置表格(10k行X 10K cols).

i am trying to transpose a table (10k rows X 10K cols) using the following script.

一个简单的数据示例

$ cat rm1

$ cat rm1

        t1      t2      t3
n1      1       2       3
n2      2       3       44
n3      1       1       1

$ sh transpose.sh rm1

$ sh transpose.sh rm1

        n1      n2      n3
t1      1       2       1
t2      2       3       1
t3      3       44      1

但是，我遇到内存错误.任何帮助，将不胜感激.

However, I am getting memory error. Any help would be appreciated.

awk -F "\t" '{
for (f = 1; f <= NF; f++)
a[NR, f] = $f
}
NF > nf { nf = NF }
END {
for (f = 1; f <= nf; f++)
for (r = 1; r <= NR; r++)
printf a[r, f] (r==NR ? RS : FS)
}'

错误

awk: cmd. line:2: (FILENAME=input FNR=12658) fatal: dupnode: r->stptr: can't allocate 10 bytes of memory (Cannot allocate memory)

推荐答案

正如我在评论中提到的那样，这是一种实现方法.在这里，我展示了一个很小的12r x 10c文件上的机制，但是我还用了不到一分钟的时间在一个10K x 10K文件上运行了1000行的数据块(Mac Powerbook).6

Here's one way to do it, as I mentioned in my comments, in chunks. Here I show the mechanics on a tiny 12r x 10c file, but I also ran a chunk of 1000 rows on a 10K x 10K file in not much more than a minute (Mac Powerbook).6

编辑以下内容已更新，以考虑行和列数不相等的M x N矩阵.以前的版本仅适用于"N x N"矩阵.

EDIT The following was updated to consider an M x N matrix with unequal number of rows and columns. The previous version only worked for an 'N x N' matrix.

$ cat et.awk
BEGIN {
    start = chunk_start
    limit = chunk_start + chunk_size - 1
}

{
    n = (limit > NF) ? NF : limit
    for (f = start; f <= n; f++) {
        a[NR, f] = $f
    }
}

END {
    n = (limit > NF) ? NF : limit

    for (f = start; f <= n; f++)
      for (r = 1; r <= NR; r++)
        printf a[r, f] (r==NR ? RS : FS)
}


$ cat t.txt
10 11 12 13 14 15 16 17 18 19
20 21 22 23 24 25 26 27 28 29 
30 31 32 33 34 35 36 37 38 39 
40 41 42 43 44 45 46 47 48 49 
50 51 52 53 54 55 56 57 58 59 
60 61 62 63 64 65 66 67 68 69 
70 71 72 73 74 75 76 77 78 79 
80 81 82 83 84 85 86 87 88 89 
90 91 92 93 94 95 96 97 98 99 
A0 A1 A2 A3 A4 A5 A6 A7 A8 A9 
B0 B1 B2 B3 B4 B5 B6 B7 B8 B9 
C0 C1 C2 C3 C4 C5 C6 C7 C8 C9 


$ cat et.sh
inf=$1
outf=$2

rm -f $outf
for i in $(seq 1 2 12); do
    echo chunk for rows $i $(expr $i + 1)
    awk -v chunk_start=$i -v chunk_size=2 -f et.awk $inf >> $outf
done



$ sh et.sh t.txt t-transpose.txt
chunk for rows 1 2
chunk for rows 3 4
chunk for rows 5 6
chunk for rows 7 8
chunk for rows 9 10
chunk for rows 11 12


$ cat t-transpose.txt 
10 20 30 40 50 60 70 80 90 A0 B0 C0
11 21 31 41 51 61 71 81 91 A1 B1 C1
12 22 32 42 52 62 72 82 92 A2 B2 C2
13 23 33 43 53 63 73 83 93 A3 B3 C3
14 24 34 44 54 64 74 84 94 A4 B4 C4
15 25 35 45 55 65 75 85 95 A5 B5 C5
16 26 36 46 56 66 76 86 96 A6 B6 C6
17 27 37 47 57 67 77 87 97 A7 B7 C7
18 28 38 48 58 68 78 88 98 A8 B8 C8
19 29 39 49 59 69 79 89 99 A9 B9 C9

然后在大文件上运行第一个块，如下所示:

And then running the first chunk on the huge file looks like:

$ time awk -v chunk_start=1 -v chunk_size=1000 -f et.awk tenk.txt  > tenk-transpose.txt

real    1m7.899s
user    1m5.173s
sys     0m2.552s

在下一个chunk_start设置为1001的情况下执行十次，依此类推(当然，将>>附加到输出中)最终会给您完整的转置结果.

Doing that ten times with the next chunk_start set to 1001, etc. (and appending with >> to the output, of course) should finally give you the full transposed result.

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