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问题:

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)

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

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.

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)

EDIT Added example in/output

Keyfile: (10 random lines from file)

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

File to sort:

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*

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

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}

回答1:

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.

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

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

Or in your case:

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"

Points of note:

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).

回答2:

I'm going to add this as an answer because it does resolve the question as I posed it, notwithstanding Charles' excellent advice about the (myriad) areas I was going wrong.

Altering the above code with Charles' point about the separate awk commands, I can now invoke the following (sorry yes, it's still using paste)...

#!/bin/bash

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

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

I was missing the $ before the variable I was calling in the awk command, which is (part) of why my original code wasn't working, as well as not including the awk variable declaration in a single awk call.

Thus, bash sortandmatch.sh keyfile filetosort 3 produces the output I want:

PVCunit2_5  plu1704         PLT_01732   PLT_01732   4etv    4etv_A  39.0    12  0.00032 27.6    >4etv_A Ryanodine receptor 2; phosphorylation, cardiac, metal transport; 1.65A {Mus musculus}
PVCunit2_4  plu1705         PLT_01733   PLT_01733   3j9q    3j9q_A  99.9    7.2e-30 1.9e-34 219.0   >3j9q_A Sheath; pyocin, bacteriocin, sheath, structural protein; 3.50A {Pseudomonas aeruginosa}
XVC_pnf15   XBW1_RS06910    XBW1_RS06910    XBW1_RS06910    1fi0    1fi0_A  69.2    1.7 4.4e-05 22.8    >1fi0_A VPR protein, R ORF protein; helix, viral protein; NMR {Synthetic} SCOP: j.11.1.1
PVCcif7     PAU_01999       PAU_01967   PAU_01967   5a3a    5a3a_A  47.5    7.3 0.00019 30.9    >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*
PVClumT15   PAU_02233       PAU_02192   PAU_02192   1tdp    1tdp_A  22.1    37.0    0.00096 27.2    >1tdp_A Carnobacteriocin B2 immunity protein; four-helix bundle, antimicrobial protein; NMR {Carnobacterium maltaromaticum} SCOP: a.29.8.1
XVC_pnf3    XBW1_RS06850    XBW1_RS06850    XBW1_RS06850    3eaa    3eaa_A  87.7    0.13    3.4e-06 35.7    >3eaa_A EVPC; T6SS, unknown function; 2.79A {Edwardsiella tarda}
PVCunit1_4  afp4            PAU_02778   PAU_02778   3j9q    3j9q_A  99.9    3.6e-29 9.5e-34 214.6   >3j9q_A Sheath; pyocin, bacteriocin, sheath, structural protein; 3.50A {Pseudomonas aeruginosa}
PVCunit2_3  plu1706         PLT_01734   PLT_01734   3j9q    3j9q_A  100.0   1.6e-34 4.3e-39 253.7   >3j9q_A Sheath; pyocin, bacteriocin, sheath, structural protein; 3.50A {Pseudomonas aeruginosa}
PVClumt17   PAK_2200        PAK_01998   PAK_01998   3k8p    3k8p_C  34.7    16.0    0.00041 34.1    >3k8p_C DSL1, KLLA0C02695P; intracellular trafficking, DSL1 complex, multisubunit tethering complex, snare proteins; 2.60A {Kluyveromyces lactis}
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*