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Revision 1.3 - (download) (as text) (annotate)
Tue Jan 29 21:57:33 2008 UTC (11 years, 11 months ago) by mkubal
Branch: MAIN
Changes since 1.2: +22 -8 lines
makes index file

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 $job (@jobs){
    if($job != 13){next;} 

    my $mg_id;
    open(IN,"$jobs_dir/$job/GENOME_ID");
    while($_ = <IN>){
	chomp($_);
	$mg_id = $_;
    }
    close(IN);

    if(! -d "$jobs_dir/$job/download"){
	`mkdir $jobs_dir/$job/download`;
    };
    
    `cp $jobs_dir/$job/rp/$mg_id/Features/peg/fasta $jobs_dir/$job/download/$mg_id.protein.fa`;
    `gzip $jobs_dir/$job/download/$mg_id.protein.fa`;

    `cp $jobs_dir/$job/rp/$mg_id/assigned_functions $jobs_dir/$job/download/$mg_id.functions.txt`;
    `gzip $jobs_dir/$job/download/$mg_id.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/download/$mg_id.dna.fa`;
	    `gzip $jobs_dir/$job/download/$mg_id.dna.fa`;
	    last;
	}
    }

    open(INDEX,">$jobs_dir/$job/download/index");
    print INDEX "$mg_id.all_internal_data.tar.gz      MGRAST data directories\n";
    print INDEX "$mg_id.complete.gbk.gz       Genbank File\n";
    print INDEX "$mg_id.dna.fa.gz        Normalized DNA FASTA\n";
    print INDEX "$mg_id.functions.txt.gz Assigned Protein Functions\n";
    print INDEX "$mg_id.protein.fa.gz    Assigned Protein Sequences FASTA\n";
    close(INDEX);

    `tar -czf $jobs_dir/$job/download/$mg_id.all_internal_data.tar.gz $jobs_dir/$job/proc $jobs_dir/$job/rp/$mg_id`; 
} 

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