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#!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 db query [opts]\n\n";
unless (@ARGV) {
die $usage;
}
my $db = $ARGV[0] or die $usage;
my $query = $ARGV[1] or die $usage;
shift @ARGV;
shift @ARGV;
main: {
my $cmd = "makeblastdb -in $db -dbtype nucl";
&process_cmd($cmd) unless (-s "$db.nin"); # only build it once.
$cmd = "tblastn -db $db -query $query -seg no @ARGV";
&process_cmd($cmd);
exit(0);
}
####
sub process_cmd {
my ($cmd) = @_;
my $ret = system($cmd);
if ($ret) {
die "Error, CMD: $cmd died with ret $ret";
}
return;
}
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