Hi Monks,
I have to filter >20GB files, just pulling any line that has a user specified keyword. It processes tab delimited file and searches through each field for keyword.
I have the single threaded version here (please excuse my novice coding/commenting):
use strict;
use warnings;
use Data::Dumper;
#declarations
my @rawfile;
my $filter_count=0;
#input
open(INFILE, "<$ARGV[0]") || die "cannot open file:$!";
####
#filter file
#------------------
# parse entire file
my $header = <INFILE>; #grabbing header
chomp $header;
my @headerArray = split("\t", $header);
my $sizeheader=@headerArray;
for my $line (<INFILE>) {
chomp $line;
my @splitline = split("\t", $line);
#my $poskey = $splitline[0] . ":" . $splitline[1];
for (@splitline){
if (/^$ARGV[1]/){
$filter_count++;
push(@rawfile,$line);
}
}
}
close INFILE;
print "Completed filtering $ARGV[0]\n";
print "Found $filter_count elements\n";
my $outfilename = substr($ARGV[0],0,length($ARGV[0])-4)."_filter.txt";
print "Filtering to output file: $outfilename\n";
####
#output file
#------------------
open(OUTFILE, ">$outfilename") || die "cannot open file to write: $!";
print OUTFILE "$header\n";
for (@rawfile) {
print OUTFILE "$_\n";
}
close OUTFILE;
I hope this will be a good example to learn threading from.
Thanks!
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