Hi, jemswira!

This is no bother at all!

You mentioned that the following captured a key that wasn't in the final set:

next unless /(E7F888)\s+.+=([^\s]+)/;
 push @activline, "$1 | $2 | $activ{$1} \n" if $activ{$1};

print @activline;
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Try the following:

next unless /(E7F888)\s+.+=([^\s]+)/;
say;
exit;
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saywill print the scalar $_ which the regex operates on. By doing this, you can examine the line to verify that the matches the following regex:

/(.{6})\s+.+=([^\s]+)/
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Also, it may be that the 'key' is not being captured from $activin, since:

push @activline, "$1 | $2 | $activ{$1} \n" if $activ{$1};
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will work only if the 'key' if found in both files and the regexs which process both work as they should.

Let me know what you find...

well i ran the code and it returned this:

E7F888 Name=arid5b ;PF01388

which is correct. Well I selected the number cause it was in both files ( I manually ctrl-f ed the notepad file.

Well a lot of lines are missing from the final output. The $activ is 512 kb large and the out put is 3kb. And also @activline is missing alot when I did print @activline;. I randomly selected E7F888 from $activin and checked to make sure it was in $uniprot, so it may be another offending line of data. If I did this:

print $activ{E7F888},"\n";
for ( read_file $uniprot ) {
  next unless /(E7F888)\s+.+=([^\s]+)/;
say;    
    push @activline, "$1 | $2 | $activ{$1} \n" if $activ{$1};

}
print @activline;
  
}
print @activline;
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I got this:

PF01388
E7F888 Name=arid5b ;PF01388

E7F888 | arid5b | PF01388
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which showed that it was in %activ and that it was found in the file. But when I run through the normal code, it is not in @activ anymore.

UPDATE,

I ran the following code to check something, and not all the data is printed, I.E. A lot of lines are not pushed into the array.

#!/usr/bin/perl
use Modern::Perl;
use File::Slurp qw/read_file write_file/;

my $uniprot     = 'uniprot-sfinal.txt';
my $activin = 'Activator-PFAM.txt';
my %activ = map { s/\.\d+//g; /(.+)\s+\|\s+(.+)/ and $1=>$2; } grep/\|
+\s+\S+/,read_file $activin;
for ( read_file $uniprot ) {
    next unless /(.{6})\s+.+=([^\s]+)/;
    print $1,"\n"
     if $activ{$1};
}
print "done";
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I am sure that there are more lines that are supposed to be printed. E.G.

$uniprot:

Q801F8  Q90XZ5; Q90XZ8;Name=dmrt1 
B7ZS42  A4PBN7; B7ZS44;Name=dmrt1-b ;PF00751;PF12374
Q157S1 Name=Crtc1  Synonyms=Mect1, 
$activ:
Q801F8 | PF00751.13 PF12374.3 PF12374.3
B7ZS42 | PF00751.13 PF12374.3 PF12374.3
Q157S1 | PF12886.2 PF12885.2 PF12884.2
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I shall try to reverse the order, I.E, make a hash out of $uniprot instead of $activ and run it again.

Perhaps your data is more complex than first thought. You listed the following:

$uniprot
Q801F8  Q90XZ5; Q90XZ8;Name=dmrt1 
B7ZS42  A4PBN7; B7ZS44;Name=dmrt1-b ;PF00751;PF12374
Q157S1 Name=Crtc1  Synonyms=Mect1, 
$activ:
Q801F8 | PF00751.13 PF12374.3 PF12374.3
B7ZS42 | PF00751.13 PF12374.3 PF12374.3
Q157S1 | PF12886.2 PF12885.2 PF12884.2
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Give the above listing, are you (potentially) expecting the following (keys/values)?

Q801F8 -> PF00751 PF12374 PF12374
B7ZS42 -> PF00751 PF12374 PF12374
Q157S1 -> PF12886 PF12885 PF12884

...

Q801F8 -> dmrt1 PF00751 PF12374 PF12374
Q90XZ5 -> dmrt1 PF00751 PF12374 PF12374
Q90XZ8 -> dmrt1 PF00751 PF12374 PF12374
B7ZS42 -> dmrt1-b PF00751 PF12374 PF12374
A4PBN7 -> dmrt1-b PF00751 PF12374 PF12374
B7ZS44 -> dmrt1-b PF00751 PF12374 PF12374
Q157S1 -> Crtc1 PF12886 PF12885 PF12884
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It looks like there are multiple keys on a single $uniprot line:

Q801F8  Q90XZ5; Q90XZ8;Name=dmrt1
^^^^^^  ^^^^^^  ^^^^^^
   |       |       |
   +-------+-------+--- keys to be captured?
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If this is the case, the current regex operating on the $uniprot lines would fail.

Let me know if the script needs to capture potentially multiple keys on a single $uniprot line...