I have a file that has about 10000 SNP ids. I need to compare this file in my local directory to an Illumina array file in the Ftp server of the UCSC database, to check for overlaps.The Snp array Illumina file is in .txt.gz format. I do not want to download the file from UCSC. Is there any other way in perl. I started writing a code but I am not sure how to compare a local file to a file in the remote server without downloading. Any ideas would be helpful. Thank you 

#!/usr/bin/perl
use strict;
use warnings;
use Net::FTP;

my $ucsc = "hgdownload.cse.ucsc.edu";
my $ucscPathPrefix = "/goldenPath//hg19/database/";
my $ftp = Net::FTP->new($ucsc, Debug => 0) or die "Cannot connect to $
+ucsc: $@";
$ftp->login("anonymous",'-anonymous@') or die "Cannot login", $ftp->me
+ssage;
$ftp->binary;
$ftp->cwd($ucscPathPrefix) or die "Cannot change working directory to 
+$ucscPathPrefix", $ftp->message;

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In reply to Retrieve SNP information from UCSC genome browser by ammalu89

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