Compare three files based on columns using Perl - perl

Question

I have three files, and I need to match the first column of file 1 to the first column of file 2 and then match the second column of file 1 with the first column of file 3.
file 1:
fji01dde AIDJFMGKG
dlp02sle VMCFIJGM
cmr03lsp CKEIFJ
and so on...
file 2:
fji01dde 25 30
dlp02sle 40 50
cmr03lsp 60 70
and so on...
file 3:
AIDJFMGKG
CKEIFJ
output needs to be:
fji01dde AIDJFMGKG 25 30
cmr03lsp CKEIFJ 60 70
and so on...
I only want lines that are common in all three files.
The below code results in the following output:
AIDJFMGKG
CKEIFJ
fji01dde 25
dlp02sle 40
cmr03lsp 60
#!/usr/bin/env perl
use strict;
use warnings;
my %data;
while (<>) {
my ( $key, $value ) = split;
push( #{ $data{$key} }, $value );
}
foreach my $key ( sort keys %data ) {
if ( #{ $data{$key} } >= #ARGV ) {
print join( "\t", $key, #{ $data{$key} } ), "\n";
}
}
Any ideas? Thanks in advance!

Answer 1

OK, looking at it - your problem is with that split - because by default, it splits on whitespace. Your second file has 3 fields by that yardstick, not two.
But also - you're not actually crossreferecing the same things, so your while ( <> ) { loop isn't going to do the trick.
In file 1 - you want to check for the value.
In file2, you're checking the key (and appending the values).
In file3, you have no value, just a key.
So with that in mind:
#!/usr/bin/env perl
use strict;
use warnings;
use Data::Dumper;
#read file1 into a hash - but invert is it's value => key instead:
# 'CKEIFJ' => 'cmr03lsp',
# etc.
open( my $file1, '<', "file1.txt" ) or die $!;
my %file1_content = map { reverse split } <$file1>;
close($file1);
print Dumper \%file1_content;
#read file 2 - read keys, store the values.
#split _2_ fields, so we keep both numbers as a substring:
#e.g.:
# 'cmr03lsp' => '60 70
#',
open( my $file2, '<', "file2.txt" ) or die $!;
my %file2_content = map { split( " ", $_, 2 ) } <$file2>;
close($file2);
print Dumper \%file2_content;
#then iterate file 3, checking if:
#file1 has a matching 'key' (but inverted - as a value)
#file2 has a cross reference.
open( my $file3, '<', "file3.txt" ) or die $!;
while ( my $line = <$file3> ) {
chomp $line;
if ( $file1_content{$line}
and $file2_content{ $file1_content{$line} } )
{
print
"$file1_content{$line} $line $file2_content{$file1_content{$line}}";
}
}
close($file3);
This prints (excluding the "dumper" output):
fji01dde AIDJFMGKG 25 30
cmr03lsp CKEIFJ 60 70
When I run this code, I get an error message: "Odd number of elements in hash assignment at line 10." Also, the columns in these files are separated by tabs.
Not with that sample data you don't. But yes - if your first file has more than two words per line, this will happen.
You can unroll that loop into a while loop:
while ( <$file1> ) {
my #fields = split;
warn "Too many fields on line $. \n" if #fields > 2;
$file1_data{$fields[1]} = $fields[0];
}