How can I find the common items from two arrays fast? - arrays

Question

I am trying to findy the common lines among two tab separated files based one field.
One line of the first file:
1 52854 s64199.1 A . . . PR GT 0/0
One line of the second file:
chr1 52854 . C T 215.302 . AB=0.692308;ABP=7.18621;AC=1;AF=0.5;AN=2;AO=9;CIGAR=1X;DP=13;DPB=13;DPRA=0;EPP=3.25157;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=17.5429;PAIRED=0;PAIREDR=0.25;PAO=0;PQA=0;PQR=0;PRO=0;QA=318;QR=138;RO=4;RPP=3.25157;RPPR=5.18177;RUN=1;SAF=0;SAP=22.5536;SAR=9;SRF=1;SRP=5.18177;SRR=3;TYPE=snp;technology.illumina=1;BVAR GT:DP:RO:QR:AO:QA:GL 0/1:13:4:138:9:318:-5,0,-5
Based on the second field (52854) in this example I have a much.
Here is my code which finds the common ones, but my files are quite large and takes a lot of time.
Is there any way to speed up the process?
Thank you very much in advance.
#!/app/languages/perl/5.14.2/bin/perl
use strict;
use warnings;
my $map_file = $ARGV[0];
my $vcf_file = $ARGV[1];
open my $map_info, $map_file or die "Could not open $map_file: $!";
my #map_array = ();
my #vcf_array = ();
while( my $mline = <$map_info>) {
chomp $mline;
my #data1 = split('\t', $mline);
my $pos1 = $data1[1];
push (#map_array, $pos1);
}
open my $vcf_info, $vcf_file or die "Could not open $vcf_file: $!";
while( my $line = <$vcf_info>) {
if ($line !~ m/^#/) {
push (#vcf_array, $line);
}
}
foreach my $a (#map_array) {
chomp $a;
foreach my $b (#vcf_array) {
chomp $b;
my #data = split('\t', $b);
my $pos2 = $data[1];
my $ref2 = $data[3];
my $allele = $data[4];
my $genotype = $data[9];
if ($a == $pos2) {
print $pos2 . "\t" . $ref2. "\t".$allele."\t".$genotype. "\n";
#print "$b\n";
}
}
}

Answer 1

Here's a version that should run much faster than your own
It reads the map file and stores each pos field in hash %wanted. Then it reads through the second file and checks whether the record is in the list of wanted values. If so then it splits the record and prints the fields you require
Note that I haven't been able to test this beyond making sure that it compiles
use strict;
use warnings;
use 5.010;
use autodie;
my ( $map_file, $vcf_file ) = #ARGV;
my %wanted;
{
open my $map_fh, '<', $map_file;
while ( <$map_fh> ) {
chomp;
my $pos = ( split /\t/, $_, 3 )[1];
++$wanted{$pos};
}
}
{
open my $vcf_fh, '<', $vcf_file;
while ( <$vcf_fh> ) {
next if /^#/;
chomp;
my $pos = ( split /\t/, $_, 3 )[1];
next unless $wanted{$pos};
my ( $ref, $allele, $genotype ) = ( split /\t/ )[3, 4, 9];
print join("\t", $pos, $ref, $allele, $genotype), "\n";
}
}

Answer 2

Below please find minimal modification of your script for hash based searches
use strict;
use warnings;
my $map_file = $ARGV[0];
my $vcf_file = $ARGV[1];
my %vcf_hash;
open( my $vcf_info, $vcf_file) or die "Could not open $vcf_file: $!";
while( my $line = <$vcf_info>) {
next if $line =~ m/^#/; # Skip comment lines
chomp $line;
my (#data) = split(/\t/, $line);
die unless #data >= 10; # Check number of fields in the input line
my ($pos) = $data[1];
# $. - line number in the file
$vcf_hash{$pos}{$.} = \#data;
}
open( my $map_info, $map_file) or die "Could not open $map_file: $!";
while( my $mline = <$map_info>) {
chomp $mline;
my (#data) = split(/\t/, $mline);
die unless #data >= 2; # Check number of fields in the input line
my ($pos) = $data[1];
if( exists $vcf_hash{$pos}) {
my $hash_ref = $vcf_hash{$pos};
for my $n (sort{$a<=>$b} keys %$hash_ref) {
my $array_ref = $hash_ref->{$n};
my $pos2 = $array_ref->[1];
my $ref2 = $array_ref->[3];
my $allele = $array_ref->[4];
my $genotype = $array_ref->[9];
print $pos2 . "\t" . $ref2. "\t".$allele."\t".$genotype. "\n";
}
}
}
The script may be improved further to reduce memory use if you use huge data files.

Answer 3

There is not a need to keep your map_file in memory but just keys. It is good to make them keys in a hash which you use for existence checking. You don't have to keep your vcf_file in memory as well, but you can just make a decision to output or not.
#!/app/languages/perl/5.14.2/bin/perl
use strict;
use warnings;
use autodie;
use constant KEY => 1;
use constant FIELDS => ( 1, 3, 4, 9 );
my ( $map_file, $vcf_file ) = #ARGV;
my %map;
{
my $fh;
open $fh, '<', $map_file;
while (<$fh>) {
$map{ ( split /\t/, $_, KEY + 2 )[KEY] } = undef;
}
}
{
my $fh;
open $fh, '<', $vcf_file;
while (<$fh>) {
next if /^#/;
chomp;
my #data = split /\t/;
print join "\t", #data[FIELDS] if exists $map{ $data[KEY] };
}
}