Xrfgtjtk

I have a file which looks like this

   18DMA      H 9996   0.886   5.687   5.320

   18DMA      H 9997   1.019   5.764   5.247

   18DMA     Np 9998   0.947   5.584   5.151

   18DMA      H 9999   1.033   5.541   5.113

   18DMA     Cn10000   0.880   5.674   5.050

   18DMA      H10001   0.831   5.616   4.971

   18DMA      H10002   0.814   5.751   5.091

   18DMA      H10003   0.957   5.735   5.003

   18DMA     Cn10004   0.837   5.486   5.185

The desire output is to delete column 3 however since from a certain row/line and next there is no a space between atom name and number I cannot make the deletion by column. Is there any way to make the deletion by selecting certain number of characters? The desire output should be

   18DMA      H    0.886   5.687   5.320

   18DMA      H    1.019   5.764   5.247

   18DMA     Np    0.947   5.584   5.151

   18DMA      H    1.033   5.541   5.113

   18DMA     Cn    0.880   5.674   5.050

   18DMA      H    0.831   5.616   4.971

   18DMA      H    0.814   5.751   5.091

   18DMA      H    0.957   5.735   5.003

   18DMA     Cn    0.837   5.486   5.185

Use cut in character mode:

cut -c1-15,21-

you may need to tweak the exact character numbers.
Again, this assumes the input doesn't use TABs (t characters) as delimiters (which it probably doesn't, since then you wouldn't have the problem of the joined fields in the first place).

If there are tabs, then the expand program can convert them to spaces.

Assuming you don't have <TAB>s but multiple spaces as field separators, and by looking at and counting your sample data, I came up with

  $ sed -E 's/^(.{15}).{5}/1/' file

   18DMA      H   0.886   5.687   5.320

   18DMA      H   1.019   5.764   5.247

   18DMA     Np   0.947   5.584   5.151

   18DMA      H   1.033   5.541   5.113

   18DMA     Cn   0.880   5.674   5.050

   18DMA      H   0.831   5.616   4.971

   18DMA      H   0.814   5.751   5.091

   18DMA      H   0.957   5.735   5.003

   18DMA     Cn   0.837   5.486   5.185

It's using a "back reference" for the first 15 characters to restore them using 1
in the replacement part of the substitute command.

$ awk -v OFS='t' 'NF == 5 { sub("[0-9]*$", "", $2) } NF == 6 { $0 = $1 OFS $2 OFS $4 OFS $5 OFS $6 } { print }' file

18DMA   H       0.886   5.687   5.320

18DMA   H       1.019   5.764   5.247

18DMA   Np      0.947   5.584   5.151

18DMA   H       1.033   5.541   5.113

18DMA   Cn      0.880   5.674   5.050

18DMA   H       0.831   5.616   4.971

18DMA   H       0.814   5.751   5.091

18DMA   H       0.957   5.735   5.003

18DMA   Cn      0.837   5.486   5.185

This short awk program will do different things to the input line depending on whether it contains 5 or 6 whitespace-delimited fields.

If it contains five fields, it removes all digits from the end of the second fields and leaves the rest as it is. If it contains six fields, it rewrites the line but omits the third field.

The output will be tab-delimited (or delimited by whatever you set OFS to on the command line).

What about using vim?

vim +"%s/([A-Za-z])@<=s?d+//g" +"w file1" +"q!" file

this regex in the vim command finds the exact pattern, deletes them and saves the file as file1 and quits vim. Your desired formatted things are now in file1.

See, vim is ultimately poor man's sed,awk,perl -e 's/.../',tr,cut and many more altogether.

NB: This will also work with vi. The slash before the bang ( ! ) escapes the bang. The regex is vim-flavored.

If I were you, I would first "fix" the original, and then simply delete the column. You can do both in a single pass, though:

awk '{sub(/[0-9]+/," &",$2); $0=$0; $3=""; print}' input_file



18DMA H  0.886 5.687 5.320

18DMA H  1.019 5.764 5.247

18DMA Np  0.947 5.584 5.151

18DMA H  1.033 5.541 5.113

18DMA Cn  0.880 5.674 5.050

18DMA H  0.831 5.616 4.971

18DMA H  0.814 5.751 5.091

18DMA H  0.957 5.735 5.003

18DMA Cn  0.837 5.486 5.185

The $0=$0 assignment will cause awk to recompute (and re-split) the current line. Unlike all other answers, this only make assumptions about the possible format of the 2nd field, not about the length or the number of the fields.

A version that will use Tab as the output field separator:

awk -vOFS='t' '{sub(/[0-9]+/," &",$2); $0=$0; $3=""; sub(OFS OFS,OFS); print}' input_file



18DMA   H       0.886   5.687   5.320

18DMA   H       1.019   5.764   5.247

18DMA   Np      0.947   5.584   5.151

18DMA   H       1.033   5.541   5.113

18DMA   Cn      0.880   5.674   5.050

18DMA   H       0.831   5.616   4.971

18DMA   H       0.814   5.751   5.091

18DMA   H       0.957   5.735   5.003

18DMA   Cn      0.837   5.486   5.185

The extra sub(OFS OFS, OFS) will collapse the empty field created by $3="". That should only be necessary if the file is to be processed by a tool which is specifically expecting tab-delimited fields, or for esthetical reasons.