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Make change to variable value inside of awk script

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# 1  
Old 02-06-2018
Make change to variable value inside of awk script
Hello,

I have text data that looks like this,
Code:
  Mrv16a3102061815532D          

  6  6  0  0  0  0            999 V2000
   -0.4018    1.9634    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1163    1.5509    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1163    0.7259    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4018    0.3134    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3127    0.7259    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3127    1.5509    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  1  6  2  0  0  0  0
M  END
>  <id>
1
>  <name>
pyridine
>  <mw>
79.102
$$$$

I have the following awk code that looks for the > <name> tag, stores the value on the next line, and then writes it to the first line of the file.

Code:
# name field tag to look for
name_field='<name>'
# value to add to beginning of name string
pre='ID_'
awk -v find_name=$name_field -v pre=$pre ' { OUT[++CNT] = $0 }
                                      F==1 { NAME = pre$0; F = 0 }
                            $0 ~ find_name { F = 1 }
                              $0 == "$$$$" { print NAME; for(i=2; i<=CNT; i++) print OUT[i]; delete OUT; CNT = 0 }
                                         ' > $output_file_name

The results look like this,
Code:
ID_pyridine
  Mrv16a3102061815532D          

  6  6  0  0  0  0            999 V2000
   -0.4018    1.9634    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1163    1.5509    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1163    0.7259    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4018    0.3134    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3127    0.7259    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3127    1.5509    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  1  6  2  0  0  0  0
M  END
>  <id>
1
>  <name>
pyridine
>  <mw>
79.102
$$$$

I have a problem with later code in cases where there are spaces in the value of <name> and I would like to substitute underscore for space in the value of NAME in the above awk code before it is written. Is there a way to do this?

Thanks,

LMHmedchem
# 2  
Old 02-06-2018
Code:
F==1 { gsub(" ", "_"); NAME = pre$0; F = 0 }

This User Gave Thanks to rdrtx1 For This Post:
LMHmedchem
# 3  
Old 02-06-2018
Because the gsub() runs on $0 here (no 3rd argument --> $0), you can alter the other output as well, by placing the { OUT[++CNT] = $0 } after it.
This User Gave Thanks to MadeInGermany For This Post:
LMHmedchem
# 4  
Old 02-06-2018
Thanks, that worked well.

This is the revised code,
Code:
# name field tag to look for
name_field='<name>'
# value to add to beginning of name string
pre='ID_'
awk -v find_name=$name_field -v pre=$pre ' { OUT[++CNT] = $0 }
                                      F==1 { gsub(" ", "_"); NAME = pre$0; F = 0 }
                            $0 ~ find_name { F = 1 }
                              $0 == "$$$$" { print NAME; for(i=2; i<=CNT; i++) print OUT[i]; delete OUT; CNT = 0 }
                                         ' > $output_file_name

It's nice to know how to do that as I'm sure it won't be the last time it comes up. Is gsub() part of awk or a call to a different tool?

Quote:
Originally Posted by MadeInGermany
Because the gsub() runs on $0 here (no 3rd argument --> $0), you can alter the other output as well, by placing the { OUT[++CNT] = $0 } after it.
Thanks for the tip, in this case, the name line is the only one that I need to modify.

---------- Post updated at 07:31 PM ---------- Previous update was at 05:07 PM ----------

Perhaps I spoke too soon about not needing to make space replacements in other places in the code. What I need to do is use the space replaced version of NAME on the first line as the original code does, and also use it for the line following the <name> tag.

I was thinking something like this,
Code:
awk -v find_name=$name_field -v pre=$pre ' { if(F == 1) { gsub(" ", "_"); NAME = pre$0; F = 0; OUT[++CNT] = NAME }
                                             else { OUT[++CNT] = $0 }
                                           }
                            $0 ~ find_name { F = 1 }
                              $0 == "$$$$" { print NAME; for(i=2; i<=CNT; i++) print OUT[i]; delete OUT; CNT = 0 }
                                         ' > $output_file_name

I think this will work but perhaps a more generalized solution would be better to allow for substitution on any requested line but not the entire input.

LMHmedchem
# 5  
Old 02-06-2018
In original post, swap lines:
Code:
F==1 { gsub(" ", "_"); NAME = pre$0; F = 0 }
     { OUT[++CNT] = $0 }

This User Gave Thanks to rdrtx1 For This Post:
LMHmedchem
# 6  
Old 02-07-2018
Quote:
Originally Posted by rdrtx1
In original post, swap lines:
Code:
F==1 { gsub(" ", "_"); NAME = pre$0; F = 0 }
     { OUT[++CNT] = $0 }

This works, as does the suggestion I posted above. I'm not sure which is preferable except that the suggestion of rdrtx1 does not require the conditional.

I assume that in the above case gsub() is changing the value of $0?

LMHmedchem
# 7  
Old 02-07-2018
Quote:
Originally Posted by LMHmedchem
This works, as does the suggestion I posted above. I'm not sure which is preferable except that the suggestion of rdrtx1 does not require the conditional.

I assume that in the above case gsub() is changing the value of $0?

LMHmedchem
Yes, the gsub() call modifies $0 if no third argument is specified. MadeInGermany already said this in post #3 in this thread. (And, you quoted it and thanked him for that tip in post #4.)
This User Gave Thanks to Don Cragun For This Post:
LMHmedchem
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