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comparison miRPlant.pl @ 50:7b5a48b972e9 draft

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author big-tiandm
date Fri, 05 Dec 2014 00:11:02 -0500
parents f008ab2cadc6
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49:f008ab2cadc6 50:7b5a48b972e9
15 use File::Basename; 15 use File::Basename;
16 #use RNA; 16 #use RNA;
17 #use Term::ANSIColor; 17 #use Term::ANSIColor;
18 18
19 my %opts; 19 my %opts;
20 GetOptions(\%opts,"i:s@","tag:s@","format=s","gfa=s","pre=s","mat=s","rfam:s","dis:i","flank:i","mfe:f","idx:s","idx2:s","mis:i","r:i","v:i","e:i","f:i","a:s","M:i","t:i","min:i","max:i","o:s","path:s","D","h"); 20 GetOptions(\%opts,"i:s@","tag:s@","phred:i","format=s","gfa=s","pre=s","mat=s","rfam:s","dis:i","flank:i","mfe:f","idx:s","idx2:s","mis:i","r:i","v:i","e:i","f:i","a:s","M:i","t:i","min:i","max:i","o:s","path:s","D","h");
21 if (!(defined $opts{i} and defined $opts{format} and defined $opts{gfa} and defined $opts{pre} and defined $opts{mat}) || defined $opts{h}) { #necessary arguments 21 if (!(defined $opts{i} and defined $opts{format} and defined $opts{gfa} and defined $opts{pre} and defined $opts{mat}) || defined $opts{h}) { #necessary arguments
22 &usage; 22 &usage;
23 } 23 }
24 24
25 my $time=&Time(); 25 my $time=&Time();
31 #&printErr(); 31 #&printErr();
32 die "Parameter \"-format\" is error! Parameter is fastq, fq, fasta or fa\n"; 32 die "Parameter \"-format\" is error! Parameter is fastq, fq, fasta or fa\n";
33 } 33 }
34 34
35 my $phred_qv=64; 35 my $phred_qv=64;
36 36 if (defined $opts{'phred'}) {
37 $phred_qv=$opts{'phred'};
38 }
37 39
38 my @inputfiles=@{$opts{'i'}}; 40 my @inputfiles=@{$opts{'i'}};
39 my @inputtags=@{$opts{'tag'}}; 41 my @inputtags=@{$opts{'tag'}};
40 42
41 my $mypath=`pwd`; 43 my $mypath=`pwd`;