how to remplace a names in a file by keys with hash

zelman796 has asked for the wisdom of the Perl Monks concerning the following question:

Hello everyone, I need your help, I have a file like this:

>1
AACTCTGGGACAATGGCACACGGGAAACAGATAATGAACGATCAGCACAGGGAACTAGCG
>2
AACTCTGGGACAATGGCACACGGGAAACAGATAATGAACGATCAGCACAGGGAACTAGCG
>3
AACTCTGGGACAATGGCACACGGGAAACAGATAATGAACGATCAGCACAGGGAACTAGCG
[download]

And I would like to change all the numbers by a list of words, I made the next program with perl but I am new using the program and I dont know who is wrong with that.

%lista2=(
1    =>    "CAT00.3",
2    =>    "CAT43.1",
3    =>    "CAT40.3"
);

open(OA,">file2.txt");

foreach $key (keys %lista2){
open(SAL,"file.txt");
while(<SAL>) {
        chomp;
            if(/>/) {
            @w=split("\t");            
                $r=0;
                s/\;//g;
                if (/%lista2[i]/) {                
                    print OA "$_ $lista2{$key}\n" ;
                    $r=1;
                    }
                }
            }
            
        }
close(SAL);
close(OA);
[download]

I would to get this:

>CAT00.3
AACTCTGGGACAATGGCACACGGGAAACAGATAATGAACGATCAGCACAGGGAACTAGCG
>CAT43.1
AACTCTGGGACAATGGCACACGGGAAACAGATAATGAACGATCAGCACAGGGAACTAGCG
>CAT40.3
AACTCTGGGACAATGGCACACGGGAAACAGATAATGAACGATCAGCACAGGGAACTAGCG
[download]

But Idont know how do that.

Comment on how to remplace a names in a file by keys with hash Select or Download Code

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Re: how to remplace a names in a file by keys with hash by Cristoforo (Curate) on Apr 27, 2018 at 22:21 UTC
Hello Your program is full of errors, some of which would have been caught if you had at the top of your program: `use strict; use warnings;` [download] Rather than going through your program to note the errors and some useless statements, I will post a correct program and you will see how it should look. #!/usr/bin/perl use strict; use warnings; my %lista2 = ( 1 => "CAT00.3", 2 => "CAT43.1", 3 => "CAT40.3" ); # open filehandle for reading (check that open was successful or die) open my $AL, '<', 'file.txt' or die $!; # open filehandle for writing (check that open was successful or die) open my $OA, '>', 'file2.txt' or die $!; while (my $line = <$AL>) { if ($line =~ /^>(\d+)$/) { my $key = $1; if (exists $lista2{$key}) { $line =~ s/$key/$lista2{$key}/; } } print $OA $line; } close $AL or die $!; close $OA or die $!; [download] Note that it does not loop through the keys like you do. And it only opens the file for reading once (the main loop). As for what's inside your while loop, there doesn't seem to be any reason for the different actions you have taken. Most don't make sense. Instead of using the default variable '$_' to read in the input in the while loop, I assigned the line being read to '$line' and this was just for clarity for this example. If I were writing the program myself, I would've probably relied on the default variable '$_' instead. Since I am using 'strict', I have to declare all the variables (with my ...) when they are first mentioned.	[reply] [d/l] [select]
Re: how to remplace a names in a file by keys with hash by LanX (Saint) on Apr 27, 2018 at 22:14 UTC
you can simply substitute a number into the hash-value `s/^>(\d+)/$lista2{$1}/` the following demonstration is safer because it is also catching missing hash entries `use strict; use warnings; my %lista2= ( 1 => "CAT00.3", 2 => "CAT43.1", 3 => "CAT40.3" ); while (<DATA>) { s/^>(\d+)/$lista2{$1} \|\| die "unknown number $1"/e; print } __DATA__ >1 AACTCTGGGACAATGGCACACGGGAAACAGATAATGAACGATCAGCACAGGGAACTAGCG >2 AACTCTGGGACAATGGCACACGGGAAACAGATAATGAACGATCAGCACAGGGAACTAGCG >3 AACTCTGGGACAATGGCACACGGGAAACAGATAATGAACGATCAGCACAGGGAACTAGCG >4` [download] `unknown number 4 at d:/Users/lanx/pm/hash_regex.pl line 14, <DATA> lin +e 7. CAT00.3 AACTCTGGGACAATGGCACACGGGAAACAGATAATGAACGATCAGCACAGGGAACTAGCG CAT43.1 AACTCTGGGACAATGGCACACGGGAAACAGATAATGAACGATCAGCACAGGGAACTAGCG CAT40.3 AACTCTGGGACAATGGCACACGGGAAACAGATAATGAACGATCAGCACAGGGAACTAGCG Compilation exited abnormally with code 255 at Sat Apr 28 00:16:17` [download] Cheers Rolf _{(addicted to the Perl Programming Language and ☆☆☆☆ :) Wikisyntax for the Monastery} update just noticed, the `s/^>(\d+)/$lista2{$1}/` variant will already warn you. `Use of uninitialized value within %lista2 in substitution iterator at hash_regex.pl line 14, <DATA> line 7.`	[reply] [d/l] [select]
Re: how to replace a names in a file by keys with hash by haukex (Archbishop) on Apr 28, 2018 at 08:52 UTC
Crossposted to StackOverflow. Crossposting is ok, but it is considered polite to inform about it so that efforts are not duplicated. Also, in your StackOverflow post you show the numbers in the input data as "`>;1;`". Which is it?	[reply] [d/l]

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