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Re^8: incrementing already existing file

by wanttoprogram (Novice)
on Mar 02, 2011 at 21:12 UTC ( [id://891095]=note: print w/replies, xml ) Need Help??


in reply to Re^7: incrementing already existing file
in thread incrementing already existing file

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

[download]

Replies are listed 'Best First'.
Re^9: incrementing already existing file
by broomduster (Priest) on Mar 02, 2011 at 23:11 UTC
    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

      [download]
    • 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"; }
}

      [download]
    • Now you can print the result: 
      say join "\t", @fields;    # separates fields with TAB

      [download]

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

[reply]
[d/l]
[select]
      #!/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;

      [download]
      I am still getting values from B from MYFILE
[reply]
[d/l]
        In this section of your code: 
        while ( <MYFILE> ) {
    chomp;
    my( $label, $index, $value ) = ( split /\s+/ )[3, 5, -1];
    
    $a_vals[ $index ] = $value;
    $b_vals[ $index ] = $value;
}

        [download]
        You need to check the value of $index to get the values for type 'A' into @a_vals, similarly for the 'B' values. The way you have it, you only get 'B' values because they are the last ones in MYFILE, and you are putting the same things into both @a_vals and @b_vals. Since the 'B' values come in last, they overwrite the corresponding 'A' values in @a_vals. You can use the same kind of if/elsif/else logic as in your other loop to fix this(but see comments below on ways to improve that).

        Now for this part of the loop over NEWF: 

        if ($label eq "A"){
$fields[-2] = $a_vals[ $index ]
    
   }
   if ($label eq "B"){
$fields[-2] = $b_vals[ $index ]

        [download]

        You should use if / elsif / else here: 

        if ($label eq "A") {
    $fields[-2] = $a_vals[ $index ]
}
elsif ($label eq "B") {
    $fields[-2] = $b_vals[ $index ]
}
else {
    print "OOPS!  bad label\n";  # complain if something is fishy
}

        [download]

        You're getting there.

[reply]
[d/l]
[select]

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