如何在linux中加入具有所需列的文件？

我有很多文件，例如在目錄“結果”中

58052 results/TB1.genes.results
198003 results/TB1.isoforms.results
58052 results/TB2.genes.results
198003 results/TB2.isoforms.results
58052 results/TB3.genes.results
198003 results/TB3.isoforms.results
58052 results/TB4.genes.results
198003 results/TB4.isoforms.results

例如：TB1.genes.results 文件如下所示：

gene_id transcript_id(s)        length  effective_length        expected_count  TPM     FPKM
ENSG00000000003 ENST00000373020,ENST00000494424,ENST00000496771,ENST00000612152,ENST00000614008 2206.00 1997.20 1.00    0.00    0.01
ENSG00000000005 ENST00000373031,ENST00000485971 940.50  731.73  0.00    0.00    0.00
ENSG00000000419 ENST00000371582,ENST00000371584,ENST00000371588,ENST00000413082,ENST00000466152,ENST00000494752 977.15  768.35  1865.00 14.27   37.82
ENSG00000000457 ENST00000367770,ENST00000367771,ENST00000367772,ENST00000423670,ENST00000470238 3779.11 3570.31 1521.00 2.50    6.64
ENSG00000000460 ENST00000286031,ENST00000359326,ENST00000413811,ENST00000459772,ENST00000466580,ENST00000472795,ENST00000481744,ENST00000496973,ENST00000498289 1936.74 1727.94 1860.00 6.33    16.77
ENSG00000000938 ENST00000374003,ENST00000374004,ENST00000374005,ENST00000399173,ENST00000457296,ENST00000468038,ENST00000475472 2020.10 1811.30 6846.00 22.22   58.90
ENSG00000000971 ENST00000359637,ENST00000367429,ENST00000466229,ENST00000470918,ENST00000496761,ENST00000630130 2587.83 2379.04 0.00    0.00    0.00
ENSG00000001036 ENST00000002165,ENST00000367585,ENST00000451668 1912.64 1703.85 1358.00 4.69    12.42
ENSG00000001084 ENST00000229416,ENST00000504353,ENST00000504525,ENST00000505197,ENST00000505294,ENST00000509541,ENST00000510837,ENST00000513939,ENST00000514004,ENST00000514373,ENST00000514933,ENST00000515580,ENST00000616923      2333.50 2124.73 1178.00 3.26    8.64

其他文件也有相同的列。要將所有帶有“gene_id”和“expected_count”列的“genes.results”加入到一個文本文件中，我給出了以下命令。

paste results/*.genes.results | tail -n+2 | cut -f1,5,12,19,26 > final.genes.rsem.txt

[-f1 (gene_id), 5 (expected_count column from TB1.genes.results), 12 (expected_count column from TB2.genes.results), 
19 (expected_count column from TB3.genes.results), 26 (expected_count column from TB4.genes.results)]

“final.genes.rsem.txt”從每個文件中選擇了gene_id 和expected_count 列。

ENSG00000000003 1.00    0.00    3.00    2.00
ENSG00000000005 0.00    0.00    0.00    0.00
ENSG00000000419 1865.00 1951.00 5909.00 8163.00
ENSG00000000457 1521.00 1488.00 849.00  1400.00
ENSG00000000460 1860.00 1616.00 2577.00 2715.00
ENSG00000000938 6846.00 5298.00 1.00    2.00
ENSG00000000971 0.00    0.00    6159.00 7069.00
ENSG00000001036 1358.00 1186.00 6196.00 7009.00
ENSG00000001084 1178.00 1186.00 631.00  1293.00

我的問題是 - 因為我只有很少的樣本，所以我在命令中給出了列號

$$ like this in “cut” -f1,5,12,19,26 $$. 如果我有超過 100 個樣本，我應該怎麼做。如何將它們加入所需的列？

使用 GNU awk。我將此命令放在 bash 腳本中。會更方便。

用法： ./join_files.sh或者，為了漂亮的列印，做：./join_files.sh | column -t。

#!/bin/bash

gawk '
NR == 1 {
   PROCINFO["sorted_in"] = "@ind_num_asc";
   header = $1;
}

FNR == 1 {
   file = gensub(/.*\/([^.]*)\..*/, "\\1", "g", FILENAME); 
   header = header OFS file;   
}

FNR > 1 {
   arr[$1] = arr[$1] OFS $5;
}

END {
   print header;

   for(i in arr) {
       print i arr[i];
   }
}' results/*.genes.results

輸出（我創建了三個內容相同的文件進行測試）

$ ./join_files.sh | column -t
gene_id          TB1      TB2      TB3
ENSG00000000003  1.00     1.00     1.00
ENSG00000000005  0.00     0.00     0.00
ENSG00000000419  1865.00  1865.00  1865.00
ENSG00000000457  1521.00  1521.00  1521.00
ENSG00000000460  1860.00  1860.00  1860.00
ENSG00000000938  6846.00  6846.00  6846.00
ENSG00000000971  0.00     0.00     0.00
ENSG00000001036  1358.00  1358.00  1358.00
ENSG00000001084  1178.00  1178.00  1178.00

說明- 添加了註釋的相同程式碼。另外，看看man gawk.

gawk '
# NR - the total number of input records seen so far.
# If the total line number is equal 1

NR == 1 {
   # If the "sorted_in" element exists in PROCINFO, then its value controls 
   # the order in which array elements are traversed in the (for in) loop.
   # else the order is undefined.

   PROCINFO["sorted_in"] = "@ind_num_asc";

   # Each field in the input record may be referenced by its position: $1, $2, and so on.
   # $1 - is the first field or the first column. 
   # The first field in the first line is the "gene_id" word;
   # Assign it to the header variable.

   header = $1;
}

# FNR - the input record number in the current input file.
# NR is the total lines counter, FNR is the current file lines counter.
# FNR == 1 - if it is the first line of the current file.

FNR == 1 {
   # remove from the filename all unneeded parts by the "gensub" function
   # was - results/TB1.genes.results
   # become - TB1

   file = gensub(/.*\/([^.]*)\..*/, "\\1", "g", FILENAME); 

   # and add it to the header variable, concatenating it with the 
   # previous content of the header, using OFS as delimiter.
   # OFS - the output field separator, a space by default.

   header = header OFS file;   
}

# some trick is used here.
# $1 - the first column value - "gene_id"
# $5 - the fifth column value - "expected_count"
FNR > 1 {
   # create array with "gene_id" indexes: arr["ENSG00000000003"], arr["ENSG00000000419"], so on.
   # and add "expected_count" values to it, separated by OFS.
   # each time, when the $1 equals to the specific "gene_id", the $5 value will be
   # added into this array item.

   # Example:
   # arr["ENSG00000000003"] = 1.00
   # arr["ENSG00000000003"] = 1.00 2.00
   # arr["ENSG00000000003"] = 1.00 2.00 3.00

   arr[$1] = arr[$1] OFS $5;
}

END {
   print header;

   for(i in arr) {
       print i arr[i];
   }
}' results/*.genes.results

引用自：https://unix.stackexchange.com/questions/395138