comparison matching.pl @ 0:07745c0958dd draft

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author big-tiandm
date Thu, 18 Sep 2014 21:40:25 -0400
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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
13 my %opts;
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
16 &usage;
17 }
18
19 my $filein=$opts{'i'};
20 my $fileout=$opts{'o'};
21 unless ($fileout=~/\/$/) {$fileout.="/";}
22 my $genome=$opts{'g'};
23 my $mis=defined $opts{'v'}? $opts{'v'} : 0;
24 my $hits=defined $opts{'r'}? $opts{'r'} : 25;
25 my $index=defined $opts{'index'} ? $opts{'index'} : "";
26 my $threads=defined $opts{'p'} ? $opts{'p'} : 1;
27
28
29 #my $time=time();
30 #my $mapdir=$fileout."/genome_match_".$time;
31 my $mapdir=$fileout."/genome_match";
32 mkdir $mapdir;
33 chdir $mapdir;
34 ###check genome index
35 if (-s $index.".1.ebwt") {
36 }else{
37 `bowtie-build $genome genome`;
38 $index="genome";
39 }
40
41 ### genome mapping
42 `bowtie -v $mis -f -p $threads -m $hits -a --best --strata $index $filein --al genome_mapped.fa --un genome_not_mapped.fa > genome_mapped.bwt`;
43
44 #`convert_bowtie_to_blast.pl genome_mapped.bwt genome_mapped.fa $genome > genome_mapped.bst`;
45
46 sub usage{
47 print <<"USAGE";
48 Version $version
49 Usage:
50 $0 -i -o
51 options:
52 -i input file# input reads fasta/fastq file
53 -g input file# genome file
54 -index file-prefix #(must be indexed by bowtie-build) The parameter
55 string must be the prefix of the bowtie index. For instance, if
56 the first indexed file is called 'h_sapiens_37_asm.1.ebwt' then
57 the prefix is 'h_sapiens_37_asm'.##can be null
58 -v <int> report end-to-end hits w/ <=v mismatches; ignore qualities,default 0;
59
60 -p/--threads <int> number of alignment threads to launch (default: 1)
61
62 -r int a read is allowed to map up to this number of positions in the genome
63 default is 25
64
65 -o output directory
66
67 -h help
68 USAGE
69 exit(1);
70 }
71