comparison rfam.pl @ 47:c75593f79aa9 draft

Uploaded

46:ca05d68aca13

use strict;
use Getopt::Long;
use File::Basename;

my %opts;
GetOptions(\%opts,"i=s","ref=s","index:s","v:i","p:i","o=s","time:s","h");
if (!(defined $opts{i} and defined $opts{o} ) || defined $opts{h}) { #necessary arguments
&usage;
}

my $filein=$opts{'i'};

	mkdir $dir;
}


my $time=Time();
if (defined $opts{'time'}) {
	$time=$opts{'time'};
}
my $mapdir=$dir."/rfam_match_".$time;
if(not -d $mapdir){
	mkdir $mapdir;
}
chdir $mapdir;
###check genome index

-v <int>           report end-to-end hits w/ <=v mismatches; ignore qualities,default 0;

-p/--threads <int> number of alignment threads to launch (default: 1)

-o output directory 
-time sting #make directory time,default is the local time
-h help
USAGE
exit(1);
}

47:c75593f79aa9

use strict;
use Getopt::Long;
use File::Basename;

my %opts;
GetOptions(\%opts,"i=s","ref=s","index:s","v:i","p:i","o=s","h");
if (!(defined $opts{i} and defined $opts{o} ) || defined $opts{h}) { #necessary arguments
&usage;
}

my $filein=$opts{'i'};

	mkdir $dir;
}


my $time=Time();

my $mapdir=$dir."/rfam_match";
if(not -d $mapdir){
	mkdir $mapdir;
}
chdir $mapdir;
###check genome index

-v <int>           report end-to-end hits w/ <=v mismatches; ignore qualities,default 0;

-p/--threads <int> number of alignment threads to launch (default: 1)

-o output directory 
-h help
USAGE
exit(1);
}