Re^7: incrementing already existing file

[broomduster]

With your program Newfile is replaced by B set of values. How do I make it to take A set first and go to B set.

So what you have is two collections of numbers in the file you open as MYFILE. One set is labeled 'A' in column 3 and the other is labeled 'B' in column 3. The values in column 5 are an index, and the values in the last column are the ones you need to collect and add to NEWF.

What I said before is still mostly what you need to do. Here's a revised outline of the code you need to write:

• Declare two arrays, one to hold the values from lines where column 3 is 'A' and another for lines where column 3 is 'B'. Something like:

  my( @a_vals, @b_vals );
  

• Read each line from MYFILE, use split to take it apart:

  my( $type, $index, $value ) = ( split /\s+/ )[2, 4, -1];
  

• Now you just put $value into the appropriate array by checking what $type is. An easy way to do that is with if/else, but I'm going to let you figure out the details. If you have Perl 5.10 or later, a nice way to handle this is with given/when.
• Now change the while ( <NEWF> ) loop to insert the collected values where you want them. You get to figure out that part, as well.

You didn't show a sample of what the output should look like, so this is as far as I can go with what you've posted. If the output should have both 'A' and 'B' values at the end of a line, you do one thing. If you need two lines (one for each of the 'A' and 'B' values), you do something different. But we can't know unless you tell us. Which leads me to the following advice about how to get along well on PerlMonks:

• Show your code. You did that. ++
• Show sample data. You did that, but we had to ask more than once. And this last time, you posted way more data than necessary to show a typical sample. About five lines of each of the 'A' and 'B' types would have been enough.
• Show the output you're getting and the output you want. You did that after we asked the first time, but when you came back with more questions and I asked for sample input and sample output, you posted input but no sample output.

I think you have enough additional information now to "fix" my code to do what you want. Give it a shot and come back with questions if you run into trouble.

[wanttoprogram]

Sorry about not being clear. I could not figure out. Thank you.

My MYFILE looks like: It has two sets of values. Column 3 has A and B

IN CHAIN A RESIDUE   1 HAS ENERGY 28.8216
IN CHAIN A RESIDUE   2 HAS ENERGY 24.9274
IN CHAIN A RESIDUE   3 HAS ENERGY 19.0884

IN CHAIN B RESIDUE   1 HAS ENERGY 29.2508
IN CHAIN B RESIDUE   2 HAS ENERGY 28.0677
IN CHAIN B RESIDUE   3 HAS ENERGY 18.4152


My NEWF looks like:  It has two sets of values. Last column has A and 
+B

ATOM      1  N   MET     1       4.751  25.841 -14.267  1.00  0.00    
+  A   
ATOM      2  HT1 MET     1       4.805  25.474 -15.239  1.00  0.00    
+  A   
ATOM      3  HT2 MET     1       4.342  26.797 -14.278  1.00  0.00    
+  A   
ATOM     21  HN  ALA     2       7.312  24.620 -11.539  1.00  0.00    
+  A   
ATOM     22  CA  ALA     2       6.858  25.683  -9.839  1.00  0.00    
+  A   
ATOM     23  HA  ALA     2       6.844  26.753  -9.694  1.00  0.00    
+  A   
ATOM     24  CB  ALA     2       5.754  24.998  -9.007  1.00  0.00    
+  A   
ATOM     36  OG1 THR     3      11.141  27.554  -8.457  1.00 93.20    
+  A   
ATOM     37  HG1 THR     3      10.623  27.711  -9.249  1.00  0.00    
+  A   
ATOM     38  CG2 THR     3      11.584  25.728  -9.911  1.00 91.24    
+  A   
ATOM     39 HG21 THR     3      12.484  26.243 -10.310  1.00  0.00    
+  A 
  
ATOM   8104  N   MET     1      -6.496 -26.244 -13.291  1.00  0.00    
+  B   
ATOM   8105  HT1 MET     1      -6.452 -26.200 -14.329  1.00  0.00    
+  B   
ATOM   8106  HT2 MET     1      -5.949 -27.077 -12.992  1.00  0.00    
+  B   
ATOM   8123  N   ALA     2      -8.788 -26.130 -10.521  1.00  0.00    
+  B   
ATOM   8124  HN  ALA     2      -9.227 -25.264 -10.749  1.00  0.00    
+  B   
ATOM   8125  CA  ALA     2      -9.147 -26.653  -9.220  1.00  0.00    
+  B   
ATOM   8126  HA  ALA     2      -9.475 -27.676  -9.335  1.00  0.00    
+  B   
ATOM   8127  CB  ALA     2      -7.979 -26.598  -8.218  1.00  0.00    
+  B   
ATOM   8133  N   THR     3     -11.093 -26.367  -7.736  1.00 86.23    
+  B   
ATOM   8134  HN  THR     3     -10.807 -27.207  -7.281  1.00  0.00    
+  B   
ATOM   8135  CA  THR     3     -12.402 -25.826  -7.360  1.00 88.87    
+  B   
ATOM   8136  HA  THR     3     -12.432 -24.774  -7.602  1.00  0.00    
+  B   


The last column values of MYFILE should be copied and repeated in last
+ but one column of my output. The two sets must be repeated.
My output looks like:

ATOM      1  N   MET     1       4.751  25.841 -14.267  1.00 28.8216  
+  A   
ATOM      2  HT1 MET     1       4.805  25.474 -15.239  1.00 28.8216  
+  A   
ATOM      3  HT2 MET     1       4.342  26.797 -14.278  1.00 28.8216  
+  A   
ATOM     21  HN  ALA     2       7.312  24.620 -11.539  1.00 24.9274  
+  A   
ATOM     22  CA  ALA     2       6.858  25.683  -9.839  1.00 24.9274  
+  A   
ATOM     23  HA  ALA     2       6.844  26.753  -9.694  1.00 24.9274  
+  A   
ATOM     24  CB  ALA     2       5.754  24.998  -9.007  1.00 24.9274  
+  A   
ATOM     36  OG1 THR     3      11.141  27.554  -8.457  1.00 19.0884  
+  A   
ATOM     37  HG1 THR     3      10.623  27.711  -9.249  1.00 19.0884  
+  A   
ATOM     38  CG2 THR     3      11.584  25.728  -9.911  1.00 19.0884  
+  A   
ATOM     39 HG21 THR     3      12.484  26.243 -10.310  1.00 19.0884  
+  A
   
ATOM   8104  N   MET     1      -6.496 -26.244 -13.291  1.00 29.2508  
+  B   
ATOM   8105  HT1 MET     1      -6.452 -26.200 -14.329  1.00 29.2508  
+  B   
ATOM   8106  HT2 MET     1      -5.949 -27.077 -12.992  1.00 29.2508  
+  B   
ATOM   8123  N   ALA     2      -8.788 -26.130 -10.521  1.00 28.0677  
+  B   
ATOM   8124  HN  ALA     2      -9.227 -25.264 -10.749  1.00 28.0677  
+  B   
ATOM   8125  CA  ALA     2      -9.147 -26.653  -9.220  1.00 28.0677  
+  B   
ATOM   8126  HA  ALA     2      -9.475 -27.676  -9.335  1.00 28.0677  
+  B   
ATOM   8127  CB  ALA     2      -7.979 -26.598  -8.218  1.00 28.0677  
+  B   
ATOM   8133  N   THR     3     -11.093 -26.367  -7.736  1.00 18.4152  
+  B   
ATOM   8134  HN  THR     3     -10.807 -27.207  -7.281  1.00 18.4152  
+  B   
ATOM   8135  CA  THR     3     -12.402 -25.826  -7.360  1.00 18.4152  
+  B   
ATOM   8136  HA  THR     3     -12.432 -24.774  -7.602  1.00 18.4152  
+  B

[broomduster]

Show us the code you tried. For that desired output, the modifications to the code I posted are not that complicated, especially with the suggestions that I already made. What I already said about collecting values from MYFILE will still work. Here are some additional hints to create the output you want:
• For each line from NEWF, you need to check the index in column 5 and the A/B label in the last column. You get your hands on each of those with something like this:

  my @fields = ( split /\s+/ );           # need to hold on to all field
  +s for later
  my( $index, $label ) = @fields[4, -1];  # this is an array slice
  

• Now that you know the index and the label for a line, you use them to find the proper value from one of the arrays you created while reading from MYFILE (e.g., @a_vals or @b_vals if you followed my example). As I mentioned, before, you can use if/else to do that but a nicer way is with given/when (as long as your Perl is 5.10.0 or newer). Here's a suggestion but note that it will not work as written here. $x and $y are not declared. You need to replace them with the correct value from @a_vals or @b_vals (HINT: use $index from above).

  use 5.010;
  
  given( $label ) {
      when ( 'A' ) { $fields[ -2 ] = $x; }
      when ( 'B' ) { $fields[ -2 ] = $y; }
      default { say "OOPS!  bad label"; }
  }
  

• Now you can print the result:

  say join "\t", @fields;    # separates fields with TAB
  

That's all there is to it. Give it another go and post back with your code if you need more help.

[wanttoprogram]

#!/usr/bin/env perl

use strict;
use warnings;


my $file1 = "2hgs_d00_internal_nrg_e.dat";
my $file2 = "2HGS_bio_conv-min_p.pdb";



open( MYFILE, '<', $file1 ) or die "cannot open $file1: $!";
open( NEWF,   '<', $file2 ) or die "cannot open $file2: $!";



my (@a_vals, @b_vals);

while ( <MYFILE> ) {
    chomp;
    my( $label, $index, $value ) = ( split /\s+/ )[3, 5, -1];
    
    $a_vals[ $index ] = $value;
    $b_vals[ $index ] = $value;
    
    
}

close MYFILE;

while ( <NEWF> ) {
    chomp;
    my @fields = ( split /\s+/ );
    my $index = $fields[4];
    my $label = $fields[-1];
    
if ($label eq "A"){
$fields[-2] = $a_vals[ $index ]
    
   }
   if ($label eq "B"){
$fields[-2] = $b_vals[ $index ]
    
   }
    my $output = join "\t", @fields;
    print  "$output\n";


}   
close NEWF;

I am still getting values from B from MYFILE