Merging two tables including multiple ocurrence of column identifiers and unique lines

Question

I asked a similar question yesterday (Merging two tables including multiple ocurrence of column identifiers) but ran into a problem with unique lines.

I would like to merge two tables based on column 1:

File 1:

1 today
1 green
2 tomorrow
3 red

File 2:

1 a lot
1 sometimes
2 at work
2 at home
2 sometimes
3 new
4 a lot
5 sometimes
6 at work

Desired output (file 3):

1 today a lot
1 today sometimes
1 green a lot
1 green sometimes
2 tomorrow at work
2 tomorrow at home
2 tomorrow sometimes
3 red new

I came up with the following:

awk -F '[\t]' -v OFS='\t' '{i=$1;$1=x} NR==FNR{A[i]=$0;next} A[i]{print i,$0A[i]}' file2 file1 > file3

However, it gives me only:

1 today sometimes
2 tomorrow sometimes
3 red new

Please note that the solutions in the previous thread (join and awk) would give me a combination of the 2 files including all lines. I would like to have only the lines of file 1 (column 1 as the identifier) but report all matching occurrences in file 2.

Edit:

columns are tab separated

Real File 1: fig|395961.4.peg.2627 Bacteria Cyanobacteria unknown unknown 1795

(Column1: fig... Column2: Bacteria... Column3 1795)

Real File 2: fig|1000561.3.peg.1838 Cysteine desulfurase (EC 2.8.1.7) Test - Thiamin Cofactors, Vitamins, Prosthetic Groups, Pigments

(Column1: fig... Column2: Cysteine... Column3 Test...)

Answer 1

I would do this in Perl:

#!/usr/bin/env perl 
use strict;

my (%file1,%file2);

## Open the 1st file
open(A,"file1");
while(<A>){
    ## Remove trailing newlines
    chomp; 
    ## Split the current line on tabs into the @F array.
    my @F=split(/\t/); 
    ## This is the tricky part. It adds fields 2-last
    ## to the hash $file1. The value of this hash is an array
    ## and the keys are the 1st fields. This will result in a list
    ## of all 1st fields and all their associated columns.
    push @{$file1{$F[0]}},@F[1..$#F];
} 


## Open the 2nd file
open(B,"file2");
while(<B>){
    ## Remove trailing newlines
    chomp; 
    ## Split the current line on tabs into the @F array.
    my @F=split(/\t/); 

    ## If the current 1st field was found in file1
    if (defined($file1{$F[0]})) {
        ## For each of the columns associated with
        ## this 1st field in the 1st file.
        foreach my $col (@{$file1{$F[0]}}) {
            print "$F[0]\t$col\t@F[1..$#F]\n";
        }
    }
} 

You could golf it into a (long) one-liner:

$ perl -lane 'BEGIN{open(A,"file1"); while(<A>){chomp; @F=split(/\t/); 
                    push @{$k{$F[0]}},@F[1..$#F];}  } 
              $k{$F[0]} && print "$F[0]\t@{$k{$F[0]}}\t@F[1..$#F]"' file2
1   today green a lot
1   today green sometimes
2   tomorrow    at work
2   tomorrow    at home
2   tomorrow    sometimes
3   red new

If you're working with huge files, let it run a while.

Answer 2

Using awk

USING FUNCTIONS

Legible:

    awk 'function get(file,x,y) {
        while ( (getline < file) > 0) {if ($1==x)y,substr($0,index($0," ")+1)}
        close(file)
        }
        ARGV[1]==FILENAME{get(ARGV[2],$1,$0)}' file1 file2

Single Line:

awk 'function g(f,x,y){while((getline <f)>0)if($1==x){print y,substr($0,index($0," ")+1)}close(f)}NR==FNR{g(ARGV[2],$1,$0)}' file1 file2

.

USING AN ARRAY

awk 'FNR==NR{a[$0]=$1;next}{for(i in a)if(a[i]==$1)print i,substr($0,index($0," ")+1)}' file file2

.

RESULT

1 today a lot
1 today sometimes
1 green a lot
1 green sometimes
2 tomorrow at work
2 tomorrow at home
2 tomorrow sometimes
3 red new

Answer 3

Whats wrong with the join command ?

join file1 file2

Gives the required result