Perl merging 2 csv files line by line with a primary key

Question

Edit: solution added.

Hi, I currently have some working albeit slow code.

It merges 2 CSV files line by line using a primary key. For example, if file 1 has the line:

"one,two,,four,42"

and file 2 has this line;

"one,,three,,42"

where in 0 indexed $position = 4 has the primary key = 42;

then the sub: merge_file($file1,$file2,$outputfile,$position);

will output a file with the line:

"one,two,three,four,42";

Every primary key is unique in each file, and a key might exist in one file but not in the other (and vice versa)

There are about 1 million lines in each file.

Going through every line in the first file, I am using a hash to store the primary key, and storing the line number as the value. The line number corresponds to an array[line num] which stores every line in the first file.

Then I go through every line in the second file, and check if the primary key is in the hash, and if it is, get the line from the file1array and then add the columns I need from the first array to the second array, and then concat. to the end. Then delete the hash, and then at the very end, dump the entire thing to file. (I am using a SSD so I want to minimise file writes.)

It is probably best explained with a code:

sub merge_file2{
 my ($file1,$file2,$out,$position) = ($_[0],$_[1],$_[2],$_[3]);
 print "merging: \n$file1 and \n$file2, to: \n$out\n";
 my $OUTSTRING = undef;

 my %line_for;
 my @file1array;
 open FILE1, "<$file1";
 print "$file1 opened\n";
 while (<FILE1>){
      chomp;
      $line_for{read_csv_string($_,$position)}=$.; #reads csv line at current position (of key)
      $file1array[$.] = $_; #store line in file1array.
 }
 close FILE1;
 print "$file2 opened - merging..\n";
 open FILE2, "<", $file2;
 my @from1to2 = qw( 2 4 8 17 18 19); #which columns from file 1 to be added into cols. of file 2.
 while (<FILE2>){
      print "$.\n" if ($.%1000) == 0;
      chomp;
      my @array1 = ();
      my @array2 = ();
      my @array2 = split /,/, $_; #split 2nd csv line by commas

      my @array1 = split /,/, $file1array[$line_for{$array2[$position]}];
      #                            ^         ^                  ^
      # prev line  lookup line in 1st file,lookup hash,     pos of key
      #my @output = &merge_string(\@array1,\@array2); #merge 2 csv strings (old fn.)

      foreach(@from1to2){
           $array2[$_] = $array1[$_];
      }
      my $outstring = join ",", @array2;
      $OUTSTRING.=$outstring."\n";
      delete $line_for{$array2[$position]};
 }
 close FILE2;
 print "adding rest of lines\n";
 foreach my $key (sort { $a <=> $b } keys %line_for){
      $OUTSTRING.= $file1array[$line_for{$key}]."\n";
 }

 print "writing file $out\n\n\n";
 write_line($out,$OUTSTRING);
}

The first while is fine, takes less than 1 minute, however the second while loop takes about 1 hour to run, and I am wondering if I have taken the right approach. I think it is possible for a lot of speedup? :) Thanks in advance.

---

Solution:

sub merge_file3{
my ($file1,$file2,$out,$position,$hsize) = ($_[0],$_[1],$_[2],$_[3],$_[4]);
print "merging: \n$file1 and \n$file2, to: \n$out\n";
my $OUTSTRING = undef;
my $header;

my (@file1,@file2);
open FILE1, "<$file1" or die;
while (<FILE1>){
    if ($.==1){
        $header = $_;
        next;
    }
    print "$.\n" if ($.%100000) == 0;
    chomp;
    push @file1, [split ',', $_];
}
close FILE1;

open FILE2, "<$file2" or die;
while (<FILE2>){
    next if $.==1;
    print "$.\n" if ($.%100000) == 0;
    chomp;
    push @file2, [split ',', $_];
}
close FILE2;

print "sorting files\n";
my @sortedf1 = sort {$a->[$position] <=> $b->[$position]} @file1;
my @sortedf2 = sort {$a->[$position] <=> $b->[$position]} @file2;   
print "sorted\n";
@file1 = undef;
@file2 = undef;
#foreach my $line (@file1){print "\t [ @$line ],\n";    }

my ($i,$j) = (0,0);
while ($i < $#sortedf1 and $j < $#sortedf2){
    my $key1 = $sortedf1[$i][$position];
    my $key2 = $sortedf2[$j][$position];
    if ($key1 eq $key2){
        foreach(0..$hsize){ #header size.
            $sortedf2[$j][$_] = $sortedf1[$i][$_] if $sortedf1[$i][$_] ne undef;
        }
        $i++;
        $j++;
    }
    elsif ( $key1 < $key2){
        push(@sortedf2,[@{$sortedf1[$i]}]);
        $i++;
    }
    elsif ( $key1 > $key2){ 
        $j++;
    }
}

#foreach my $line (@sortedf2){print "\t [ @$line ],\n"; }

print "outputting to file\n";
open OUT, ">$out";
print OUT $header;
foreach(@sortedf2){
    print OUT (join ",", @{$_})."\n";
}
close OUT;

}

Thanks everyone, the solution is posted above. It now takes about 1 minute to merge the whole thing! :)

Answer 1

Two techniques come to mind.

1. Read the data from the CSV files into two tables in a DBMS (SQLite would work just fine), and then use the DB to do a join and write the data back out to CSV. The database will use indexes to optimize the join.

2. First, sort each file by primary key (using perl or unix sort), then do a linear scan over each file in parallel (read a record from each file; if the keys are equal then output a joined row and advance both files; if the keys are unequal then advance the file with the lesser key and try again). This step is O(n + m) time instead of O(n * m), and O(1) memory.