为awk列说明符传递bash变量 [英] passing bash variable for awk column specifier

问题描述

有很多关于将shell变量传递给awk的线程，我已经很容易地弄明白了，但是我要传递的变量是列说明符变量($1,$2等)

There are loads of threads about passing a shell variable to awk, and I've figured that out easily enough, but the variable I want to pass is the column specifier variable ($1,$2 etc)

考虑到shell也将这些变量用作默认的命令行参数变量，这令人困惑.

Given that the shell uses these variables as default command line argument variables as well, this is getting confusing.

在此脚本中，我只是将2个文件排序并连接在一起，但是为了开始泛化该脚本，我希望能够在命令行上指定awk应该在密钥文件中的字段作为其排序说明符.

In this script I'm just sorting and joining 2 files together, but in order to begin generalising the script a little, I want to be able to specify on the command line, the field in the key file that awk should be taking as its sort-specifier.

我在这里做错了什么? (我只是刚开始接触awk，而oneliner从

What am I doing wrong here? (I'm only just getting to grips with awk and the oneliner was adapted slightly from here.

keyfile="$1"
filetosort="$2"
field="$3"

awk -v a="$field"
paste "$keyfile" <(awk 'NR==FNR{o[FNR]=a; next} {t[$1]=$0} END{for(x=1; x<=FNR; x++){y=o[x]; print t[y]}}' $keyfile $filetosort)

编辑在/输出中添加了示例

EDIT Added example in/output

密钥文件:(来自文件的10条随机行)

PVClumt18   PAK_2199    PAK_01997
PVClopt2    PAK_2091    PAK_01895
PVCcif7     PAK_1975    PAK_01793
PVClopT12   PAU_02101   PAU_02063
PVCpnf20    PAK_3524    PAK_03184
PVClopt3    PAK_2090    PAK_01894
PVClopT11   PAU_02102   PAU_02064
PVCunit2_11 plu1698     PLT_01726
PVClumT9    afp10       PAU_02198
PVCunit2_17 plu1692     PLT_01720

要排序的文件:

PAU_02064   1pqx    1pqx_A  37.4    13  0.00035 31.4    >1pqx_A Conserved hypothetical protein; ZR18,structure, autostructure,spins,autoassign, northeast structural genomics consortium; NMR {Staphylococcus aureus subsp} SCOP: d.267.1.1 PDB: 2ffm_A 2m6q_A 2m8w_A
PAK_01997   5ftj    5ftj_A  99.9    1.6e-26 4.2e-31 229.2   >5ftj_A Transitional endoplasmic reticulum ATPase; hydrolase, single-particle, AAA ATPase; HET: ADP OJA; 2.30A {Homo sapiens} PDB: 3cf1_A* 3cf3_A* 3cf2_A* 5ftk_A* 5ftl_A* 5ftm_A* 5ftn_A* 1r7r_A* 5c19_A 5c1b_A* 5c18_A* 3cf0_A*
PAK_01894   3j9q    3j9q_A  99.9    1.8e-29 4.6e-34 215.9   >3j9q_A Sheath; pyocin, bacteriocin, sheath, structural protein; 3.50A {Pseudomonas aeruginosa}
PAK_03184   1xju    1xju_A  99.4    4.1e-17 1.1e-21 98.8    >1xju_A Lysozyme; secreted inactive conformation, hydrolase; 1.07A {Enterobacteria phage P1} SCOP: d.2.1.3
PAK_01793   5a3a    5a3a_A  50.8    6   0.00016 31.4    >5a3a_A SIR2 family protein; transferase, P-ribosyltransferase, metalloprotein, NAD-depen lipoylation, regulatory enzyme, rossmann fold; 1.54A {Streptococcus pyogenes} PDB: 5a3b_A* 5a3c_A*
PLT_01720   3ggm    3ggm_A  54.2    4.9 0.00013 26.2    >3ggm_A Uncharacterized protein BT9727_2919; bacillus cereus group., structural genomics, PSI-2, protein structure initiative; 2.00A {Bacillus thuringiensis serovarkonkukian}
PLT_01726   3h2t    3h2t_A  96.8    8e-06   2.1e-10 82.6    >3h2t_A Baseplate structural protein GP6; viral protein, virion; 3.20A {Enterobacteria phage T4} PDB: 3h3w_A 3h3y_A
PAK_01895   3j9q    3j9q_A  100.0   2.5e-35 6.4e-40 248.6   >3j9q_A Sheath; pyocin, bacteriocin, sheath, structural protein; 3.50A {Pseudomonas aeruginosa}
PAU_02198   4jiv    4jiv_D  69.6    1.6 4.2e-05 27.5    >4jiv_D VCA0105, putative uncharacterized protein; PAAR-repeat motif, membrane piercing, type VI secretion SYST vibrio cholerae VGRG2; HET: PLM STE ELA; 1.90A {Vibrio cholerae o1 biovar eltor}
PAU_02063   4yap    4yap_A  31.1    20  0.00052 29.1    >4yap_A Glutathione S-transferase homolog; GSH-lyase GSH-dependent; 1.11A {Sphingobium SP} PDB: 4g10_A 4yav_A*

因此，我需要根据密钥文件中的第3列和文件中的第1列对行进行排序和匹配.

Thus I need to sort and match the rows based on column 3 in the keyfile, and column 1 in the file to sort.

以及生成的文件:(第3列和第4列的重复是我打算在之后进行整理的内容)

And the resulting file: (The duplication of columns 3 & 4 was something I was planning to sort out after)

PVClumt18   PAK_2199    PAK_01997   PAK_01997   5ftj    5ftj_A  99.9    1.6e-26 4.2e-31 229.2   >5ftj_A Transitional endoplasmic reticulum ATPase; hydrolase, single-particle, AAA ATPase; HET: ADP OJA; 2.30A {Homo sapiens} PDB: 3cf1_A* 3cf3_A* 3cf2_A* 5ftk_A* 5ftl_A* 5ftm_A* 5ftn_A* 1r7r_A* 5c19_A 5c1b_A* 5c18_A* 3cf0_A*
PVClopt2    PAK_2091    PAK_01895   PAK_01895   3j9q    3j9q_A  100.0   2.5e-35 6.4e-40 248.6   >3j9q_A Sheath; pyocin, bacteriocin, sheath, structural protein; 3.50A {Pseudomonas aeruginosa}
PVCcif7 PAK_1975    PAK_01793   PAK_01793   5a3a    5a3a_A  50.8    6   0.00016 31.4    >5a3a_A SIR2 family protein; transferase, P-ribosyltransferase, metalloprotein, NAD-depen lipoylation, regulatory enzyme, rossmann fold; 1.54A {Streptococcus pyogenes} PDB: 5a3b_A* 5a3c_A*
PVClopT12   PAU_02101   PAU_02063   PAU_02063   4yap    4yap_A  31.1    20  0.00052 29.1    >4yap_A Glutathione S-transferase homolog; GSH-lyase GSH-dependent; 1.11A {Sphingobium SP} PDB: 4g10_A 4yav_A*
PVCpnf20    PAK_3524    PAK_03184   PAK_03184   1xju    1xju_A  99.4    4.1e-17 1.1e-21 98.8    >1xju_A Lysozyme; secreted inactive conformation, hydrolase; 1.07A {Enterobacteria phage P1} SCOP: d.2.1.3
PVClopt3    PAK_2090    PAK_01894   PAK_01894   3j9q    3j9q_A  99.9    1.8e-29 4.6e-34 215.9   >3j9q_A Sheath; pyocin, bacteriocin, sheath, structural protein; 3.50A {Pseudomonas aeruginosa}
PVClopT11   PAU_02102   PAU_02064   PAU_02064   1pqx    1pqx_A  37.4    13  0.00035 31.4    >1pqx_A Conserved hypothetical protein; ZR18,structure, autostructure,spins,autoassign, northeast structural genomics consortium; NMR {Staphylococcus aureus subsp} SCOP: d.267.1.1 PDB: 2ffm_A 2m6q_A 2m8w_A
PVCunit2_11 plu1698 PLT_01726   PLT_01726   3h2t    3h2t_A  96.8    8e-06   2.1e-10 82.6    >3h2t_A Baseplate structural protein GP6; viral protein, virion; 3.20A {Enterobacteria phage T4} PDB: 3h3w_A 3h3y_A
PVClumT9    afp10   PAU_02198   PAU_02198   4jiv    4jiv_D  69.6    1.6 4.2e-05 27.5    >4jiv_D VCA0105, putative uncharacterized protein; PAAR-repeat motif, membrane piercing, type VI secretion SYST vibrio cholerae VGRG2; HET: PLM STE ELA; 1.90A {Vibrio cholerae o1 biovar eltor}
PVCunit2_17 plu1692 PLT_01720   PLT_01720   3ggm    3ggm_A  54.2    4.9 0.00013 26.2    >3ggm_A Uncharacterized protein BT9727_2919; bacillus cereus group., structural genomics, PSI-2, protein structure initiative; 2.00A {Bacillus thuringiensis serovarkonkukian}

推荐答案

当您传递awk -v a="$field"时，awk变量a的说明仅适用于该单个awk命令 .您不能期望a在awk的完全不同的调用中可用.

When you pass awk -v a="$field", the specification of the awk variable a is only good for that single awk command. You can't expect a to be available in a completely different invocation of awk.

因此，您需要将其直接放置在 中:

Thus, you need to put it in-place directly:

$ bashvar="2"
$ echo 'foo bar baz' | awk -v awkvar="$bashvar" '{print $awkvar}'
bar

或者您的情况:

field=1
awk -v a="$field" '
NR==FNR {
  o[FNR]=$a;
  next;
}

{ t[$1] = $0 }

END {
  for(x=1; x<=FNR; x++) {
    y=o[x]
    printf("%s\t%s\n", y, t[y])
  }
}' "$keyfile" "$filetosort"

---

要点:

---

Points of note:

• 我们的printf在这里同时发出 键和值，因此不需要使用paste将keyfile值放回去.
• $a用于将awk变量a(从shell变量field分配)视为变量名称本身，并执行间接引用-因此查找相关的列号.
• 总是，总是在扩展时引用您的shell变量.否则，您将无法知道$keyfile的扩展将为awk生成多少个参数-可能为0(如果在IFS中找不到字符串中没有字符的话)；否则，可能为0.可以是1，但也可以是一个完全不受限制的数字(input file.txt将成为两个参数，分别是input和file.txt； * input * .txt将每个*替换为文件列表).

• Our printf here is emitting both the key and the value, so there's no need to use paste to put the keyfile values back in.
• $a is used to treat the awk variable a (assigned from shell variable field) as a variable name itself, and to perform an indirect reference -- thus, looking up the relevant column number.
• Always, always quote your shell variables on expansion. Otherwise, you have no way of knowing how many argument to awk will be generated by the expansion of $keyfile -- it could be 0 (if there are no characters in the string not found in IFS); it could be 1, but it could also be a completely unbounded number (input file.txt would become two arguments, input and file.txt; * input * .txt would have each * replaced with a list of files).

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