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comparison rfam.pl @ 47:c75593f79aa9 draft

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author big-tiandm
date Wed, 03 Dec 2014 01:54:29 -0500
parents 0c4e11018934
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46:ca05d68aca13 47:c75593f79aa9
10 use strict; 10 use strict;
11 use Getopt::Long; 11 use Getopt::Long;
12 use File::Basename; 12 use File::Basename;
13 13
14 my %opts; 14 my %opts;
15 GetOptions(\%opts,"i=s","ref=s","index:s","v:i","p:i","o=s","time:s","h"); 15 GetOptions(\%opts,"i=s","ref=s","index:s","v:i","p:i","o=s","h");
16 if (!(defined $opts{i} and defined $opts{o} ) || defined $opts{h}) { #necessary arguments 16 if (!(defined $opts{i} and defined $opts{o} ) || defined $opts{h}) { #necessary arguments
17 &usage; 17 &usage;
18 } 18 }
19 19
20 my $filein=$opts{'i'}; 20 my $filein=$opts{'i'};
29 mkdir $dir; 29 mkdir $dir;
30 } 30 }
31 31
32 32
33 my $time=Time(); 33 my $time=Time();
34 if (defined $opts{'time'}) { 34
35 $time=$opts{'time'}; 35 my $mapdir=$dir."/rfam_match";
36 }
37 my $mapdir=$dir."/rfam_match_".$time;
38 if(not -d $mapdir){ 36 if(not -d $mapdir){
39 mkdir $mapdir; 37 mkdir $mapdir;
40 } 38 }
41 chdir $mapdir; 39 chdir $mapdir;
42 ###check genome index 40 ###check genome index
93 -v <int> report end-to-end hits w/ <=v mismatches; ignore qualities,default 0; 91 -v <int> report end-to-end hits w/ <=v mismatches; ignore qualities,default 0;
94 92
95 -p/--threads <int> number of alignment threads to launch (default: 1) 93 -p/--threads <int> number of alignment threads to launch (default: 1)
96 94
97 -o output directory 95 -o output directory
98 -time sting #make directory time,default is the local time
99 -h help 96 -h help
100 USAGE 97 USAGE
101 exit(1); 98 exit(1);
102 } 99 }
103 100