column replacement with awk, with retaining the fo

问题:

I have a a.pdb file as,

ATOM      1  N   ARG     1       0.000   0.000   0.000  1.00  0.00           N
ATOM      2  H1  ARG     1       0.000   0.000   0.000  1.00  0.00           H
ATOM      3  H2  ARG     1       0.000   0.000   0.000  1.00  0.00           H
ATOM      4  H3  ARG     1       0.000   0.000   0.000  1.00  0.00           H

and a.xyz file as

16.388 -5.760 -23.332
17.226 -5.608 -23.768
15.760 -5.238 -23.831
17.921 -5.926 -26.697

I want to replace 6,7 and 8th column of a.pdb with a.xyz. Once replaced, I need to maintain tabs/space/columns of a.pdb.

I have tried

awk 'NR==FNR {fld1[NR]=$1; fld2[NR]=$2; fld3[NR]=$3; next} {$6=fld1[FNR]; $7=fld2[FNR]; $8=fld3[FNR]}1' a.xyz a.pdb 

But it doesn't keep the format.

回答1:

This is exactly what the 4th arg for split() in GNU awk was invented to facilitate:

gawk '
NR==FNR { pdb[NR]=$0; next }
{
    split(pdb[FNR],flds,FS,seps)
    flds[6]=$1
    flds[7]=$2
    flds[8]=$3
    for (i=1;i in flds;i++)
        printf "%s%s", flds[i], seps[i]
    print ""
}
' a.pdb a.xyz

ATOM      1  N   ARG     1       16.388   -5.760   -23.332  1.00  0.00           N
ATOM      2  H1  ARG     1       17.226   -5.608   -23.768  1.00  0.00           H
ATOM      3  H2  ARG     1       15.760   -5.238   -23.831  1.00  0.00           H
ATOM      4  H3  ARG     1       17.921   -5.926   -26.697  1.00  0.00           H

回答2:

Not a general solution, but this might work with in this particular case:

awk 'NR==FNR{for(i=6; i<=8; i++) A[FNR,i]=$(i-5); next} {for(i=6; i<=8; i++) sub($i,A[FNR,i])}1' file2 file1

or

awk '{for(i=6; i<=8; i++) if(NR==FNR) A[FNR,i]=$(i-5); else sub($i,A[FNR,i])} NR>FNR' file2 file1

There is a bit of a shift, though. We would need to know the fields widths to prevent this.

-- Or perhaps with substrings:

awk 'NR==FNR{A[FNR]=$0; next} {print substr($0,1,p) FS A[FNR] substr($0,p+length(A[FNR]))}' p=33 file2 file1

-- changing it in the OP's original solution:

awk 'NR==FNR {fld1[NR]=$1; fld2[NR]=$2; fld3[NR]=$3; next} {sub($6,fld1[FNR]); sub($7,fld2[FNR]); sub($8,fld3[FNR])}1' file file1

with the same restrictions as the first 2 suggestions.

So 1, 2, and 4 use sub to replace, which is not a water proof solution, since earlier fields might interfere and it uses regex rather than strings (and so the regex dot happens to match the actual dot), but with this particular input, it might pan out..

Probably nr. 3 would be a more fool-proof method..

--edit-- I think this would work with the given input:

awk 'NR==FNR{A[FNR]=$1 "  " $2 " " $3; next} {print substr($0,1,p) A[FNR] substr($0,p+length(A[FNR]))}' p=32  file2 file1

but I think something like printf or sprint formatting would be required to make it fool-proof. So, perhaps something like this:

awk 'NR==FNR{A[FNR]=sprintf("%7.3f %7.3f %8.4f", $1, $2, $3); next} {print substr($0,1,p) A[FNR] substr($0,p+length(A[FNR]))}' p=31 file2 file1

or not on one line:

awk '
  NR==FNR {
    A[FNR]=sprintf("%7.3f %7.3f %8.4f", $1, $2, $3)
    next
  }
  {
    print substr($0,1,p) A[FNR] substr($0,p+length(A[FNR]))
  }
' p=31 file2 file1

回答3:

You can try this one

paste -d' '  test4 test5 |awk '{print $1,$2,$3,$4,$5,$12,$13,$14,$9,$10,$11}'