# HG changeset patch
# User big-tiandm
# Date 1406282235 14400
# Node ID b963c4a161d25ef438ccc97bd3f6739dcd8b7a5f
# Parent  d88fc3c0084e9d8129f752ac1342ab2953698df7
Deleted selected files

diff -r d88fc3c0084e -r b963c4a161d2 matching.pl
--- 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);
-}
-