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comparison rfam.pl @ 19:141a337097e1 draft

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author big-tiandm
date Fri, 25 Jul 2014 05:22:33 -0400
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18:a79212816cbc 19:141a337097e1
1 #!/usr/bin/perl -w
2 #Filename:
3 #Author: Tian Dongmei
4 #Email: tiandm@big.ac.cn
5 #Date: 2013/7/19
6 #Modified:
7 #Description:
8 my $version=1.00;
9
10 use strict;
11 use Getopt::Long;
12 use File::Basename;
13
14 my %opts;
15 GetOptions(\%opts,"i=s","ref=s","index:s","v:i","p:i","o=s","time:s","h");
16 if (!(defined $opts{i} and defined $opts{o} ) || defined $opts{h}) { #necessary arguments
17 &usage;
18 }
19
20 my $filein=$opts{'i'};
21 my $dir=$opts{'o'};
22 unless ($dir=~/\/$/) {$dir.="/";}
23 my $rfam=$opts{'ref'};
24 my $mis=defined $opts{'v'}? $opts{'v'} : 0;
25 my $index=defined $opts{'index'} ? $opts{'index'} : "";
26 my $threads=defined $opts{'p'} ? $opts{'p'} : 1;
27
28 if (not -d $dir) {
29 mkdir $dir;
30 }
31
32
33 my $time=Time();
34 if (defined $opts{'time'}) {
35 $time=$opts{'time'};
36 }
37 my $mapdir=$dir."/rfam_match_".$time;
38 if(not -d $mapdir){
39 mkdir $mapdir;
40 }
41 chdir $mapdir;
42 ###check genome index
43 if (-s $index.".1.ebwt") {
44 }else{
45 &checkACGT($rfam);
46 `bowtie-build $rfam`;
47 $index="$rfam";
48 }
49 ### genome mapping
50 `bowtie -v $mis -f -p $threads -k 1 $index $filein --al rfam_mapped.fa --un rfam_not_mapped.fa > rfam_mapped.bwt`;
51
52 sub checkACGT{
53 my $string;
54 open IN,"<$rfam";
55 while (my $aline=<IN>) {
56 if ($aline!~/^>/) {
57 $aline=~s/U/T/gi;
58 }
59 $string .=$aline;
60 }
61 close IN;
62 $rfam=basename($rfam);
63 open OUT, ">$rfam";
64 print OUT $string;
65 close OUT;
66 }
67
68 sub Time{
69 my $time=time();
70 my ($sec,$min,$hour,$day,$month,$year) = (localtime($time))[0,1,2,3,4,5,6];
71 $month++;
72 $year+=1900;
73 if (length($sec) == 1) {$sec = "0"."$sec";}
74 if (length($min) == 1) {$min = "0"."$min";}
75 if (length($hour) == 1) {$hour = "0"."$hour";}
76 if (length($day) == 1) {$day = "0"."$day";}
77 if (length($month) == 1) {$month = "0"."$month";}
78 #print "$year-$month-$day $hour:$min:$sec\n";
79 return("$year-$month-$day-$hour-$min-$sec");
80 }
81 sub usage{
82 print <<"USAGE";
83 Version $version
84 Usage:
85 $0 -i -o
86 options:
87 -i input file# input reads fasta/fastq file
88 -ref input file# rfam file, which do not contain miRNAs
89 -index file-prefix #(must be indexed by bowtie-build) The parameter
90 string must be the prefix of the bowtie index. For instance, if
91 the first indexed file is called 'h_sapiens_37_asm.1.ebwt' then
92 the prefix is 'h_sapiens_37_asm'.##can be null
93 -v <int> report end-to-end hits w/ <=v mismatches; ignore qualities,default 0;
94
95 -p/--threads <int> number of alignment threads to launch (default: 1)
96
97 -o output directory
98 -time sting #make directory time,default is the local time
99 -h help
100 USAGE
101 exit(1);
102 }
103