match a list of identifiers to another list using perl - arrays

Question

I am stuck on how to loop a list over another list. Perhaps I am not searching for the right words but I am stuck and would appreciate any help on my code.
I went over this thread but am still getting errors running my script. How do I search a Perl array for a matching string?
the database file
chr1 1692239 1692249 AH_GARP2_comp198_c0_seq1
chr1 2233934 2233944 CS_GARP2_comp323_c0_seq1
chr1 5993434 5993444 CS_GARP2_comp635_c0_seq1
chr1 6198157 6198167 CS_GARP2_comp115_c0_seq1
chr1 6465781 6465791 JB_GARP2_comp560_c0_seq1
chr1 7827923 7827933 JB_GARP2_comp855_c0_seq1
chr1 7920939 7920949 AA_GARP2_comp614_c0_seq1
chr1 7964000 7964010 CS_GARP2_comp717_c0_seq1
chr1 9314857 9314867 AH_GARP2_comp237_c0_seq1
chr1 9654532 9654542 AH_GARP2_comp632_c0_seq1
the query file
name1 CS_GARP2_comp635_c0_seq1
name2 JB_GARP2_comp855_c0_seq1
name3 AH_GARP2_comp198_c0_seq1
name4 AH_GARP2_comp237_c0_seq1
My code
#!/usr/bin/perl5.16.2
use 5.16.2;
use lib '/users/ec1/perl5/lib/perl5/';
use warnings;
use strict;
my $filename = shift; ## database
my $filename2= shift; ## list of ids
open (DB, '<', $filename ) || die "Unable to open: $!";
open (I , '<', $filename2) || die "Unable to open: $!";
my #DB;
while (<DB>) {
chomp;
my #DB = split /\t/, $_; ## define as list
#print "#DB[0,1,2,3]\n";
}
while (my $line = <I>) {
chomp $line;
my ($name, $id) = split /\t/, $line;
if ($DB[3] =~ /$id/) {print "$DB[0]\t$DB[1]\t$DB[2]\t$DB[3]\n";
} else {print "na\n"}
}

Answer 1

Put DB into hash (%DB) to ease searches.
use strict; use warnings;
my $filename = shift; ## database
my $filename2= shift; ## list of ids
my %DB;
open (DB, '<', $filename ) || die "Unable to open: $!";
while (<DB>) {
chomp;
my #row = split( /[ \t]+/, $_); ## define as list
die "expected four items in db file - line $.\n" unless #row == 4; # expect four elements in a row
die "duplicate id in db file - line $." if exists $DB{$row[3]};
$DB{$row[3]} = \#row;
}
close DB;
open (I , '<', $filename2) || die "Unable to open: $!";
while (<I>) {
chomp;
my ($name, $id) = split /[ \t]+/, $_;
if(exists ($DB{$id})) {
my #row = #{$DB{$id}};
print join("\t", #row), "\n";
} else {
print "na\n"
}
}
close(I);
P.S. I have changed split pattern to ease tests of copy&paste data file content

Answer 2

The problem with your approach is that the my #DB inside while loop creates a lexical scope so it will always contain the last line's contents and that content will not be available outside the loop.
You should read the id file in to a hash map and check if the line for db file exists as a key in hash.
#!/usr/bin/perl
use warnings;
use strict;
use autodie;
my ($dbfile, $idfile) = #ARGV;
open my $id_fh, '<', $idfile;
open my $db_fh, '<', $dbfile;
my %ids;
while (<$id_fh>) {
++$ids{$_} for (split /\s+/)[1]; # split and put column2 as key in %ids.
}
while (<$db_fh>) {
my $fld = (split /\s+/)[3]; # split and assign column4 to $fld
print "na\n" and next unless $ids{$fld}; # print "na" if fld is not in hash and move to next line
print "$_"; # print the line if column4 exits.
}