Mercurial > repos > big-tiandm > mirplant2
changeset 21:b963c4a161d2 draft
Deleted selected files
author | big-tiandm |
---|---|
date | Fri, 25 Jul 2014 05:57:15 -0400 |
parents | d88fc3c0084e |
children | c0aecae5eb03 |
files | matching.pl |
diffstat | 1 files changed, 0 insertions(+), 90 deletions(-) [+] |
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--- a/matching.pl Fri Jul 25 05:32:24 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,90 +0,0 @@ -#!/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; - -my %opts; -GetOptions(\%opts,"i=s","g=s","index:s","v:i","p:i","r:s","o=s","time: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 $genome=$opts{'g'}; -my $mis=defined $opts{'v'}? $opts{'v'} : 0; -my $hits=defined $opts{'r'}? $opts{'r'} : 25; -my $index=defined $opts{'index'} ? $opts{'index'} : ""; -my $threads=defined $opts{'p'} ? $opts{'p'} : 1; - - -my $time=&Time(); -if (defined $opts{'time'}) { - $time=$opts{'time'}; -} - -my $mapdir=$fileout."/genome_match_".$time; -if(not -d $mapdir){ - mkdir $mapdir; -} -chdir $mapdir; -###check genome index -if (-s $index.".1.ebwt") { -}else{ - `bowtie-build $genome genome`; - $index="genome"; -} - -### genome mapping -`bowtie -v $mis -f -p $threads -m $hits -a --best --strata $index $filein --al genome_mapped.fa --un genome_not_mapped.fa --max genome_mapped_Mlimit.fa > genome_mapped.bwt`; - -#`convert_bowtie_to_blast.pl genome_mapped.bwt genome_mapped.fa $genome > genome_mapped.bst`; - -sub Time{ - my $time=time(); - my ($sec,$min,$hour,$day,$month,$year) = (localtime($time))[0,1,2,3,4,5,6]; - $month++; - $year+=1900; - if (length($sec) == 1) {$sec = "0"."$sec";} - if (length($min) == 1) {$min = "0"."$min";} - if (length($hour) == 1) {$hour = "0"."$hour";} - if (length($day) == 1) {$day = "0"."$day";} - if (length($month) == 1) {$month = "0"."$month";} - #print "$year-$month-$day $hour:$min:$sec\n"; - return("$year-$month-$day-$hour-$min-$sec"); -} - -sub usage{ -print <<"USAGE"; -Version $version -Usage: -$0 -i -o -options: --i input file# input reads fasta/fastq file --g input file# genome file --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) - --r int a read is allowed to map up to this number of positions in the genome - default is 25 - --o output directory - --h help -USAGE -exit(1); -} -