Mercurial > repos > big-tiandm > mirplant2
comparison matching.pl @ 47:c75593f79aa9 draft
Uploaded
author | big-tiandm |
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date | Wed, 03 Dec 2014 01:54:29 -0500 |
parents | 0c4e11018934 |
children |
comparison
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46:ca05d68aca13 | 47:c75593f79aa9 |
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9 | 9 |
10 use strict; | 10 use strict; |
11 use Getopt::Long; | 11 use Getopt::Long; |
12 | 12 |
13 my %opts; | 13 my %opts; |
14 GetOptions(\%opts,"i=s","g=s","index:s","v:i","p:i","r:s","o=s","time:s","h"); | 14 GetOptions(\%opts,"i=s","g=s","index:s","v:i","p:i","r:s","o=s","h"); |
15 if (!(defined $opts{i} and defined $opts{o} ) || defined $opts{h}) { #necessary arguments | 15 if (!(defined $opts{i} and defined $opts{o} ) || defined $opts{h}) { #necessary arguments |
16 &usage; | 16 &usage; |
17 } | 17 } |
18 | 18 |
19 my $filein=$opts{'i'}; | 19 my $filein=$opts{'i'}; |
25 my $index=defined $opts{'index'} ? $opts{'index'} : ""; | 25 my $index=defined $opts{'index'} ? $opts{'index'} : ""; |
26 my $threads=defined $opts{'p'} ? $opts{'p'} : 1; | 26 my $threads=defined $opts{'p'} ? $opts{'p'} : 1; |
27 | 27 |
28 | 28 |
29 my $time=&Time(); | 29 my $time=&Time(); |
30 if (defined $opts{'time'}) { | 30 my $mapdir=$fileout."/genome_match"; |
31 $time=$opts{'time'}; | |
32 } | |
33 | |
34 my $mapdir=$fileout."/genome_match_".$time; | |
35 if(not -d $mapdir){ | 31 if(not -d $mapdir){ |
36 mkdir $mapdir; | 32 mkdir $mapdir; |
37 } | 33 } |
38 chdir $mapdir; | 34 chdir $mapdir; |
39 ###check genome index | 35 ###check genome index |