Re^2: how to compare column 1 to column 2 and vice versa from multiple rows.

[BhariD]

Thank you so much!! your suggestions really helped. I apologize for the formatting errors. I hope its not too bad this time.

Can I ask you one more question. With this input file (below):
gene_a gene_b
gene_b gene_a

I get the following output:
gene_a gene_b

If the input file is something like this:
gene_a gene_b
gene_b gene_a
gene_c gene_a
gene_a gene_c
gene_c gene_b
gene_b gene_c

Then I want the program to output the following:
gene_a gene_b gene_c

instead of:
gene_a gene_b
gene_b gene_c
gene_c gene_a

The thing is I am looking for pairs for which column[0] is equal to column1 and vice versa. This can happen for any combination of numbers (as I showed with three above a, b and c). Can you provide your suggestion in this case. I would really really appreciate it!

Thanks

BH

[ccn]

It is not too late to insert <code> tags into your original post. You are able to update it any time.

As I understand you just want to output unique names of genes instead of raw rows. Than try this

#!/usr/bin/perl -lan
# Usage: thisscript.pl genes.txt

if ( $seen{ join ' ', sort @F }++ ) {
    $uniq{$F[0]}++;
    $uniq{$F[1]}++;
}
END {
    print for keys %uniq;
}

And this:

Linux version:
perl -lane '@u{@F}=() if $s{join "", sort @F}++ }{ print for keys %u' 
+genes.txt

Windows version:
perl -lane "@u{@F}=() if $s{join '', sort @F}++ }{ print for keys %u" 
+genes.txt

Where genes.txt is a file containing gene rows

Feel free to ask if you need explanations on the algorithm and it's implementation.

[BhariD]

Could you please tell me what each line is doing in this code.


if ( $seen{ join ' ', sort @F }++ ) {
    $uniq{$F[0]}++;
    $uniq{$F[1]}++;
}
END {
    print for keys %uniq;
}

code: Thanks to ccn


Also, before I execute this code I fill the  @F from the file input right?


my @F = <DATA>;

[ccn]

No you don't fill @F. The -a switch does it for you. see perldoc perlrun The code above is complete script. Just run it as shown in usage.

Now explanations:

#!/usr/bin/perl -lan
# Usage: thisscript.pl genes.txt


# %seen is a hash where we store keys composed from seen rows
# @F is an array of 2 elements $F[0] is a first column of your file an
+d $F[1] is the second one (see [doc://perlrun] -a switch
# So the key for row is composed by concatenation of sorted columns

if ( $seen{ join ' ', sort @F }++ ) {

# %uniq hash will keep seen columns first and second

    $uniq{$F[0]}++;  
    $uniq{$F[1]}++;
}
# the code above is loops over each row of file because of -n switch s
+ee [doc://perlrun]

END {  # this block run just before exit
    print for keys %uniq;
}