Re: Join files using perl

[blue_cowdawg]

in reply to Join files using perl

Could somebody help me do this on a faster way? Thanks!

Faster? <shrug!> dunno, but pull up a chair. Here are the two input files..

$ cat file1.txt 
1
2
3
4
5

$ cat file2.txt 
5
4
3
2
1

and here's some code:

#!/usr/bin/perl -w 
use strict;
use Tie::File;

my ($file1,$file2,$fileout)  = @ARGV;

tie my @ry1,"Tie::File",$file1 or die "$file1:$!";
tie my @ry2,"Tie::File",$file2 or die "$file2:$!";
tie my @out,"Tie::File",$fileout or die "$fileout:$!";

@out=(@ry1,@ry2);

untie @out;
untie @ry2;
untie @ry1;

which gives you this as an output:

$ cat out.txt 
1
2
3
4
5
5
4
3
2
1

[linseyr]

Thanks, but this wasn't what I wanted. My files looks like:

ID1     50
ID2     60
ID3     100

FILE2:
ID1     20
ID2     100
ID3      10

OUTPUT:
ID1     50     20
ID2     60     100
ID3     100    10

[linseyr]

Oh and both files contain more columns, that was my main problem. How do I assign an array as values in an hash?

[linseyr]

I tried this:

foreach $line (@FILE1){
        chomp($line);
        my($ID, @values) = split("\t", $line);

        $aref = \@values;

        $common1{$ID} = $aref;


}
print $common1{"B01_05_121214_LAP_G1_87_20593"};

But the output is: ARRAY(0x7f8f4b82d310)

[blue_cowdawg]

my mistake. try this:

#!/usr/bin/perl -w 
use strict;
use Tie::File;

my ($file1,$file2,$fileout)  = @ARGV;

tie my @ry1,"Tie::File",$file1 or die "$file1:$!";
tie my @ry2,"Tie::File",$file2 or die "$file2:$!";
tie my @out,"Tie::File",$fileout or die "$fileout:$!";
my %een=();

my %dat=();
map{ $dat{$_}=[]} grep !$een{$_}++,map { (split(/[\s\t\n]+/,$_))[0] } 
+(@ry1,@ry2);
foreach my $line((@ry1,@ry2)){
        my ($key,@vals)=split(/[\s\t\n]+/,$line);
        push @{$dat{$key}},@vals;
}

         
@out=map { join("\t",($_,@{$dat{$_}})) } keys %dat;

untie @out;
untie @ry2;
untie @ry1;

Using your input files this was tested and gave output that you are looking for...

[Marshall]

Consider this:

#!/usr/bin/perl -w
use strict;

my $FILE1 = <<END;
ID1     50
ID2     60
ID3     100
END

my $FILE2 = <<END;
ID1     20
ID2     100
ID3      10
END

my %ids;

foreach my $file (\$FILE1, \$FILE2) #just put path name of
                                    #FILE1 and FILE2 here.
                                    #This ref is special because of 
                                    #putting the file contents within
                                    #the code.
                                    #FILE1 and 2 are "hereis" docs.
{
   open (FILE, "<", $file) or die "unable to open $file for read $!";
   while (<FILE>)
   {
      chomp; # delete trailing \n
      
      # here I split on one or more space characters,
      # A tab char doesn't show up well on this forum's text
      
      my ($id, $value) = split (/\s+/, $_);
      push @{$ids{$id}}, $value;
   }
}

#Each key of the hash of %ids contains a reference to
#an array of id's. This is called a HoA - Hash of Array

foreach my $id (sort keys %ids)
{
   print "$id @{$ids{$id}}\n";
}

#This code will run very fast because each line is
#only read one time - Input/Output (I/O) is very 
#"expensive" 

__END__

OUTPUT:
ID1 50 20
ID2 60 100
ID3 100 10