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Revision 1.1 - (download) (as text) (annotate)
Thu Dec 20 23:06:35 2007 UTC (11 years, 11 months ago) by mkubal
Branch: MAIN
v1

if(scalar(@ARGV) != 1){
    print "usage: prepare_metagenome_files_for_download location_of_jobs_dir\n";
    print "example: prepare_metagenome_files_for_download /vol/mg-rast/Jobs.dev\n";
    exit;
}

#$job_dirs such as /vol/mg-rast/Jobs.dev
my $jobs_dir = shift(@ARGV);


opendir(DIR,$jobs_dir);
@jobs = readdir(DIR);
close(DIR);

foreach my $job (@jobs){
    my $mg_id;
    open(IN,"$jobs_dir/$job/GENOME_ID");
    while($_ = <IN>){
	chomp($_);
	$mg_id = $_;
    }
    close(IN);
    
    `cp $jobs_dir/$job/rp/$mg_id/Features/peg/fasta $jobs_dir/$job/$mg_id.peg.fasta`;
    `cp $jobs_dir/$job/rp/$mg_id/assigned_functions $jobs_dir/$job/$mg_id.assigned_functions.txt`;
        
    opendir(DIR,"$jobs_dir/$job/proc");
    my @files = readdir(DIR);
    close(DIR);
    foreach my $file (@files){
	if($file =~/(\d+.fa)$/){
	    `cp $jobs_dir/$job/proc/$file $jobs_dir/$job/$mg_id.normalized.fasta`;
	    last;
	}
    }
    
    `tar -czf $jobs_dir/$job/$mg_id.genome_and_proc_dir.tar.gz $jobs_dir/$job/proc $jobs_dir/$job/rp/$mg_id`; 
} 

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