string match search - perl

Question

one text file like this as query file:
fooLONGcite
GetmoreDATA
stringMATCH
GOODthing
another text file like this as subject file:
sometingfooLONGcite
anyotherfooLONGcite
matchGetmoreDATA
GETGOODthing
brotherGETDATA
CITEMORETHING
TOOLONGSTUFFETC
The expected result will be get the matched string from subject file and then print it out. So, the output should be:
sometingfooLONGcite
anyotherfooLONGcite
matchGetmoreDATA
GETGOODthing
Here is my perl script. But It doesn't work. Can you help me find where is the problem? Thanks.
#!/usr/bin/perl
use strict;
# to check the command line option
if($#ARGV<0){
printf("Usage: \n <tag> <seq> <outfile>\n");
exit 1;
}
# to open the given infile file
open(tag, $ARGV[0]) or die "Cannot open the file $ARGV[0]";
open(seq, $ARGV[1]) or die "Cannot open the file $ARGV[1]";
my %seqhash = ();
my $tag_id;
my $tag_seq;
my $seq_id;
my $seq_seq;
my $seq;
my $i = 0;
print "Processing cds seq\n";
#check the seq file
while(<seq>){
my #line = split;
if($i != 0){
$seqhash{$seq_seq} = $seq;
$seq = "";
print "$seq_seq\n";
}
$seq_seq = $line[0];
$i++;
}
while(<tag>){
my #tagline = split;
$tag_seq = $tagline[0];
$seq = $seqhash{$seq_seq};
#print "$tag_seq\n";
print "$seq\n";
#print output ">$id\n$seq\n";
}
#print "Ending of Processing gff\n";
close(tag);
close(seq);

Answer 1

As I understand, you look for a match of part of the string, not an exact one. Here a script that does what I think you are looking for:
Content of script.pl. I take into account that file of queries is small because I add all its content to a regex:
use warnings;
use strict;
## Check arguments.
die qq[Usage: perl $0 <query_file> <subject_file>\n] unless #ARGV == 2;
## Open input files. Abort if found errors.
open my $fh_query, qq[<], shift #ARGV or die qq[Cannot open input file: $!\n];
open my $fh_subject, qq[<], shift #ARGV or die qq[Cannot open input file: $!\n];
## Variable to save a regex with alternations of the content of the 'query' file.
my $query_regex;
{
## Read content of the 'query' file in slurp mode.
local $/ = undef;
my $query_content = <$fh_query>;
## Remove trailing spaces and generate a regex.
$query_content =~ s/\s+\Z//;
$query_content =~ s/\n/|/g;
$query_regex = qr/(?i:($query_content))/;
}
## Read 'subject' file and for each line compare if that line matches with
## any word of the 'query' file and print in success.
while ( <$fh_subject> ) {
if ( m/$query_regex/o ) {
print
}
}
Run the script:
perl script.pl query.txt subject.txt
And result:
sometingfooLONGcite
anyotherfooLONGcite
matchGetmoreDATA
GETGOODthing

Answer 2

Your current code doesn't make a lot of sense; you're even referencing variables you don't assign anything to.
All you need to do is read the first file into a hash, then check each line of the second against that hash.
while (my $line = <FILE>)
{
chomp($line);
$hash{$line} = 1;
}
...
while (my $line = <FILE2>)
{
chomp($line);
if (defined $hash{$line})
{
print "$line\n";
}
}