Anomalous, you're right. As I wrote in my original post, I have never actually used s/foo/bar other than in a one liner. I was looking for a way to find and replace strings in a file without writing to a new output file and when the replacement strings are not the same length as the sub-strings that are replaced. Clearly I am not doing this the correct way, and if there is a correct way, I haven't been able to find/understand it yet. What I want is to open a file and if a line is:

'nc7-52:p39|read1|1|19|296|0.0642'

and change it to:

C_fraterna_nc7-52

using a hash where $hash{nc7-52}=C_fraterna_nc7-52

Update: From this example it looks like it would be easy to print to output, but some lines in the file will not be modified and I still want to preserve them.

sorry, this thread may be a bit out of control since I had too many problems to begin with

From this example it looks like it would be easy to print to output ...

As a first step, create a small test input file and just print the altered and unaltered lines to standard output, e.g.,
    print $my_new_line_what_is_just_the_way_i_want_it;
When this limited, test output looks ok, start to think about the process of opening a new file and writing to that file instead of STDOUT. When that looks ok, start thinking about all the input/output file verification and renaming that has to happen. (I'm sure there are modules to facilitate the "edit in place" process, but I don't know what they are off-hand.)

---

Give a man a fish:   <%-(-(-(-<

Please see Update and Further Update to Re: In place search and replace with a hash. (Unfortunately, we may be playing "update tag.")

---

Give a man a fish:   <%-(-(-(-<

 
open FH, "<infile.txt" or die $!;
open OUT, ">outfile.txt";
while (<FH>)
          {
          if (/(\S+):(\S+).*\n/)
               {
               $var1 = "$1";
               $var2 = "$2";
               print OUT "$var1_$var2\n"
               }
            elsif (/(.*)\n/)
                {
                print OUT "$1\n";
               }
            }
     close FH;
[download]

This does what I want in terms of preserving the input files non matching lines, but I am still getting a "use of uninitialized value" error, one for every line in the input file:

Use of uninitialized value $var1_ in concatenation (.) or string at test_perl.pl line 42

print OUT "$var1_$var2\n"


The  '_' (underscore) character is a valid identifier, i.e., variable name, symbol. Therefore, the two variables you're using are  $var1_ (note trailing _), which is not defined, and  $var2, which is. Had you been using strictures as well as warnings, Perl would not have allowed this little oversight (see strict and warnings). The proper way to write this statement (if you really need the _) is
    print OUT "${var1}_$var2\n";
(Note that I've added a ; at the end; the absence of this statement terminator caused no syntactic problem in the given code, but would have eventually — trust me.)

open FH, "<infile.txt" or die $!;
open OUT, ">outfile.txt";


Update: You seem to be back-sliding. In contrast to your OPed code, this code uses global filehandles, two-parameter open, and does not check the status of the output file open. Tsk, tsk! IMHO, the OPed code used better practices.

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Give a man a fish:   <%-(-(-(-<

Ah, thank you! I don't know why I was trying to use "_". Totally unnecessary. Now that you have helped me to fix most of these basic problems, I am back to the original problem of replacing the hash keys with the hash values. The hash is created with:

use strict;
use warnings;
open my $fh, '<', 'hash_test.txt' 
    or die "Cant open file $!";

LINE:
while (my $line = <$fh>) 
    {
        my ($key, $value) = split /\s/, $line;
        next LINE if not $key;
        $hash{$key} = $value;
        chomp (%hash);
        while ( my( $key, $value ) = each %hash )          
    }

close $fh;
[download]

Then the hash keys are searched for (and replaced with their associated values if found) in the input file using

open FH, "<infile.txt" or die $!;
open OUT, ">outfile.txt";

 while (<FH>)
          {
          if (/(\S+):(\S+).*\n/)
               {
               $var1 = "$1";
               $var2 = "$2";
               print OUT "$hash{$var1} $var2\n";
               }
            elsif (/(.*)\n/)
                {
                print OUT "$1\n";
               }
            }
     close FH;
[download]

This results in the error

Use of uninitialized value within %hash in concatenation (.) or string at test_perl.pl line 41, <FH> line 5

UPDATE I think the problem was that I had initialized my %hash inside a while loop. I moved it up to the beginning of the program, and it worked!

Thanks Anomalous, I see what you mean by backsliding- I had been testing the code with a single file to control for errors with the loop (and avoid being overwhelmed by error messages). Here is the updated code that works. I see other responses suggesting better ways to do this and potential problems with the hash, and I will address those as well. But at the moment, this works. Thanks for all your help!

#!/usr/bin/perl
use strict;
use warnings;

my %hash = ();
open my $fh, '<', 'sample_name_ID_hash.txt' or die "Cant open file $!"
+;

LINE:
while (my $line = <$fh>) 
    {
        my ($key, $value) = split /\s/, $line;
        next LINE if not $key;
        $hash{$key} = $value;
        chomp (%hash);
    }

close $fh;
        
@file_array = <*.nex> or die $!; #find all the files
foreach $file (@file_array)
    {
    my $prefix = $file;
    $prefix =~ s/\.nex//;
    open FH, "$file", or die $!;
    print "found $file with prefix $prefix\n";
    open OUT, ">out$prefix.nex" or die $!;

 while (<FH>)
          {
          if (/^\s+\'(\S+):(\S\d+)\|\w+\|(\d)\S+\'(.*)\n/)
               {
               $var1 = "$1";
               $var2 = "$2";
               $var3 = "$3";
               $var4 = "$4";
               print OUT "'$hash{$var1}_${var2}_$var3'$var4\n";
               }
            elsif (/(.*)\n/)
                {
                print OUT "$1\n";
               }
            }
     }
[download]

if (/(\S+):(\S+).*\n/)
     {
     $var1 = "$1";
     $var2 = "$2";
     print OUT "$var1_$var2\n"
     }
  elsif (/(.*)\n/)
      {
      print OUT "$1\n";
      }
     }
[download]

Ok, once you get that working (i.e., fix  $var1_ problem), try reducing the big if-statement to a single  s/// substitution (untested):
    s{ (\S) : (\S) }{${1}_$2}xmsg;
(which just replaces every : with an _), followed by a print of the (possibly altered) line (held in  $_ in this code) to the output filehandle.

Update: This reply may have been superseded by your intervening post, but what the heck...

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Give a man a fish:   <%-(-(-(-<