[Bio] / FigKernelScripts / prepare_metagenome_files_for_ftp.pl Repository:
ViewVC logotype

View of /FigKernelScripts/prepare_metagenome_files_for_ftp.pl

Parent Directory Parent Directory | Revision Log Revision Log


Revision 1.2 - (download) (as text) (annotate)
Fri Dec 21 15:09:40 2007 UTC (12 years, 5 months ago) by mkubal
Branch: MAIN
Changes since 1.1: +10 -0 lines
v2

if(scalar(@ARGV) != 2){
    print "usage: prepare_metagenome_files_for_ftp location_of_jobs_dir ftp_dir\n";
    print "example: prepare_metagenome_files_for_ftp /vol/mg-rast/Jobs.dev /vol/ftp.theseed.org/Metagenomes\n";
    exit;
}

#$jobs_dir is location of jobs to moved to ftp
my $jobs_dir = shift(@ARGV);

#$target_dir is is destination directory to be mirrored to ftp dir 
my $target_dir = shift(@ARGV);

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

foreach my $job (@jobs){
    $job = 13;
    
    if(-e "$jobs_dir/$job/PRIVATE"){next}
 
    my $mg_id;
    open(IN,"$jobs_dir/$job/GENOME_ID");
    while($_ = <IN>){
	chomp($_);
	$mg_id = $_;
    }
    close(IN);
    
    if(-e $target_dir/$mg_id.peg.fasta){ 
	if(`cmp $jobs_dir/$job/$mg_id.peg.fasta $target_dir/$mg_id.peg.fasta`){   
	    `cp $jobs_dir/$job/$mg_id.peg.fasta $target_dir/$mg_id.peg.fasta`;
	}
    }
    else{
	`cp $jobs_dir/$job/$mg_id.peg.fasta $target_dir/$mg_id.peg.fasta`;
    }
    
    if(-e $target_dir/$mg_id.assigned_functions.txt){ 
	if(`cmp $jobs_dir/$job/$mg_id.assigned_functions.txt $target_dir/$mg_id.assigned_functions.txt`){	
	    `cp $jobs_dir/$job/$mg_id.assigned_functions.txt $target_dir/$mg_id.assigned_functions.txt`;
	}
    }
    else{
	`cp $jobs_dir/$job/$mg_id.assigned_functions.txt $target_dir/$mg_id.assigned_functions.txt`;
    }
    
    if(-e $target_dir/$mg_id.genome_and_proc_dir.tar.gz){
	if(`cmp $jobs_dir/$job/$mg_id.genome_and_proc_dir.tar.gz $target_dir/$mg_id.genome_and_proc_dir.tar.gz`){
	    `cp $jobs_dir/$job/$mg_id.genome_and_proc_dir.tar.gz $target_dir/$mg_id.genome_and_proc_dir.tar.gz`; 
	}
    }
    else{
	`cp $jobs_dir/$job/$mg_id.genome_and_proc_dir.tar.gz $target_dir/$mg_id.genome_and_proc_dir.tar.gz`; 
    }

    if(-e $target_dir/$mg_id.normalized.fasta){
	if(`cmp $jobs_dir/$job/$mg_id.normalized.fasta $target_dir/$mg_id.normalized.fasta`){ 
	    `cp $jobs_dir/$job/$mg_id.normalized.fasta $target_dir/$mg_id.normalized.fasta`; 
	}
    }
    else{
	`cp $jobs_dir/$job/$mg_id.normalized.fasta $target_dir/$mg_id.normalized.fasta`; 
    }

    if(-e $target_dir/$mg_id.gbk.gz){
	if(`cmp $jobs_dir/$job/$mg_id.gbk.gz $target_dir/$mg_id.gbk.gz`){ 
	    `cp $jobs_dir/$job/$mg_id.gbk.gz $target_dir/$mg_id.gbk.gz`; 
	}
    }
    else{
	`cp $jobs_dir/$job/$mg_id.gbk.gz $target_dir/$mg_id.gbk.gz`; 
    }

    if(-e $target_dir/$mg_id.user_id_to_normalized_unique.txt){
	if(`cmp $jobs_dir/$job/$mg_id.user_id_to_normalized_unique.txt $target_dir/$mg_id.user_id_to_normalized_unique.txt`){ 
	    `cp $jobs_dir/$job/$mg_id.user_id_to_normalized_unique.txt $target_dir/$mg_id.user_id_to_normalized_unique.txt`; 
	}
    }
    else{
	`cp $jobs_dir/$job/$mg_id.user_id_to_normalized_unique.txt $target_dir/$mg_id.user_id_to_normalized_unique.txt`; 
    }

} 

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3