Mercurial > repos > big-tiandm > sirna_plant
view rfam.pl @ 8:d317cee86d4b draft
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author | big-tiandm |
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date | Thu, 23 Oct 2014 22:46:39 -0400 |
parents | 07745c0958dd |
children | 318617877a10 |
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#!/usr/bin/perl -w #Filename: #Author: Tian Dongmei #Email: tiandm@big.ac.cn #Date: 2013/7/19 #Modified: #Description: my $version=1.00; use strict; use Getopt::Long; use File::Basename; my %opts; GetOptions(\%opts,"i=s","ref=s","index:s","v:i","p:i","o=s","h"); if (!(defined $opts{i} and defined $opts{o} ) || defined $opts{h}) { #necessary arguments &usage; } my $filein=$opts{'i'}; my $fileout=$opts{'o'}; unless ($fileout=~/\/$/) {$fileout.="/";} my $rfam=$opts{'ref'}; my $mis=defined $opts{'v'}? $opts{'v'} : 0; my $index=defined $opts{'index'} ? $opts{'index'} : ""; my $threads=defined $opts{'p'} ? $opts{'p'} : 1; #my $time=time(); #my $mapdir=$fileout."/rfam_match_".$time; my $mapdir=$fileout."/rfam_match"; mkdir $mapdir; chdir $mapdir; ###check genome index if (-s $index.".1.ebwt") { }else{ &checkACGT($rfam); `bowtie-build $rfam rfam`; $index="rfam"; } #chdir "rfam_match_1397022331"; ### genome mapping `bowtie -v $mis -f -p $threads -k 1 $index $filein --al rfam_mapped.fa --un rfam_not_mapped.fa > rfam_mapped.bwt`; sub checkACGT{ my $string; open IN,"<$rfam"; while (my $aline=<IN>) { if ($aline!~/^>/) { $aline=~s/U/T/gi; } $string .=$aline; } close IN; $rfam=basename($rfam); open OUT, ">$rfam"; print OUT $string; close OUT; } sub usage{ print <<"USAGE"; Version $version Usage: $0 -i -o options: -i input file# input reads fasta/fastq file -ref input file# rfam file, which do not contain miRNAs -index file-prefix #(must be indexed by bowtie-build) The parameter string must be the prefix of the bowtie index. For instance, if the first indexed file is called 'h_sapiens_37_asm.1.ebwt' then the prefix is 'h_sapiens_37_asm'.##can be null -v <int> report end-to-end hits w/ <=v mismatches; ignore qualities,default 0; -p/--threads <int> number of alignment threads to launch (default: 1) -o output directory -h help USAGE exit(1); }