# HG changeset patch
# User big-tiandm
# Date 1406282252 14400
# Node ID 5691802f074bc6d55770423580d6c9ad342b4ec0
# Parent  45de5e1ff4872a17739ea3d5ad19a81e96567149
Deleted selected files

diff -r 45de5e1ff487 -r 5691802f074b collapseReads2Tags.pl
--- a/collapseReads2Tags.pl	Fri Jul 25 05:57:27 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,170 +0,0 @@
-#!/usr/bin/perl -w
-#Filename:
-#Author: Tian Dongmei
-#Email: tiandm@big.ac.cn
-#Date: 2014-3-20
-#Modified:
-#Description: fastq file form reads cluster(the same sequence in the same cluster)
-my $version=1.00;
-
-use strict;
-use Getopt::Long;
-
-my %opts;
-GetOptions(\%opts,"i:s@","format=s","mark:s","qual:s","qv:i","o=s","h");
-if (!(defined $opts{o} and defined $opts{'format'})  || defined $opts{h}) { #necessary arguments
-&usage;
-}
-my @filein=@{$opts{i}} if(defined $opts{i});
-my $name=defined $opts{'mark'} ? $opts{'mark'} : "seq";
-my $fileout=$opts{'o'};
-my $pq=defined $opts{'qv'} ? $opts{'qv'} : 33;
-my %hash;##分块存放原始序列
-
-my $format=$opts{'format'};
-if ($format ne "fastq" && $format ne "fq" && $format ne "fasta" && $format ne "fa") {
-	die "Parameter -format is error!\n";
-}
-
-my ($qualT,$qualV);
-if (defined $opts{'qual'} && ($format eq "fastq" || $format eq "fq")) {  #quality filter
-	my @temp=split /:/,$opts{'qual'};
-	$qualT=$temp[0];
-	$qualV=$temp[1];
-
-	for (my $i=0;$i<@filein;$i++) {
-		open IN,"<$filein[$i]";
-		while (my $aline=<IN>) {
-			my $seq=<IN>;
-			my $n=<IN>;
-			my $qv=<IN>;
-			my $tag=&qvcheck($qv,$qualT,$qualV);
-			next if(!$tag);
-			my $str=substr($seq,0,6);
-			$hash{$str}[$i].=$seq;
-		}
-		close IN;
-	}
-}
-elsif($format eq "fastq" || $format eq "fq"){ ### do not filter low quality reads
-	for (my $i=0;$i<@filein;$i++) {
-		open IN,"<$filein[$i]";
-		while (my $aline=<IN>) {
-			my $seq=<IN>;
-			my $n=<IN>;
-			my $qv=<IN>;
-			my $str=substr($seq,0,6);
-			$hash{$str}[$i].=$seq;
-		}
-		close IN;
-	}
-
-}
-elsif($format eq "fasta" || $format eq "fa"){
-	for (my $i=0;$i<@filein;$i++) {
-		open IN,"<$filein[$i]";
-		while (my $aline=<IN>) {
-			my $seq=<IN>;
-			my $str=substr($seq,0,6);
-			$hash{$str}[$i].=$seq;
-		}
-		close IN;
-	}
-}
-
-open OUT,">$fileout"; #output file  
-my $count=0;
-foreach my $key (keys %hash) {
-	my %cluster;
-	for (my $i=0;$i<@filein;$i++) {
-		next if(!(defined $hash{$key}[$i]));
-		my @tmp=split/\n/,$hash{$key}[$i];
-		foreach  (@tmp) {
-			$cluster{$_}[$i]++;
-		}
-	}
-	
-	foreach my $seq (keys %cluster) {
-		my $exp=""; my $ee=0;
-		for (my $i=0;$i<@filein;$i++) {
-			if (defined $cluster{$seq}[$i]) {
-				$exp.="_$cluster{$seq}[$i]";
-				$ee+=$cluster{$seq}[$i];
-			}else{
-				$exp.="_0";
-			}
-		}
-		$count+=$ee;
-		$exp=~s/^_//;
-		print OUT ">$name","_$count:$exp","_x$ee\n$seq\n";
-	}
-}
-close OUT;
-
-
-sub qvcheck{
-	my ($str,$t,$v)=@_;
-	my $qv=0;
-	if($t eq "mean"){ 
-		$qv=&getMeanQuality($str);
-	}
-	elsif($t eq "min"){
-		$qv=&getMinQuality($str);
-	}
-	if ($qv<$v) {
-		return 0;
-	}
-	return 1;
-}
-
-sub getMeanQuality(){
-	chomp $_[0];
-	my @bases = split(//,$_[0]);
-	my $sum = 0;
-	for(my $i = 0; $i <= $#bases; $i++){
-		my $num = ord($bases[$i]) - $pq;
-		$sum += $num;
-	}
-	
-	return $sum/($#bases+1);
-	
-}
-
-###
-### This function gives back the Q-value of the worst base
-sub getMinQuality(){
-	chomp $_[0];
-	my @bases = split(//,$_[0]);
-	my $worst = 1000;
-	for(my $i = 0; $i <= $#bases; $i++){
-#		printf ("base: $bases[$i]  --> %d\n",ord($bases[$i]));
-		my $num = ord($bases[$i]) - $pq;
-		if($num < $worst){
-			$worst = $num;
-		}
-	}
-	return $worst;
-}
-
-sub usage{
-print <<"USAGE";
-Version $version
-Usage:
-$0 -i -format -mark -qual -qv -o 
-options:
--i input file#fastq file ##can be multiple -i file1 -i file2 ...
--mark string#quary name,default is "seq"
--o output file
--format string # fastq|fasta|fq|fa
-
--qual #reads filter
-   eg:(min:value/mean:value)
-   This parameter just for solexa reads.
-   If the input files are solid and needs filter,please do filter first .
-   
--qv  integer #Phred quality64/33,default 33
--h help
-USAGE
-exit(1);
-}
-
diff -r 45de5e1ff487 -r 5691802f074b convert_bowtie_to_blast.pl
--- a/convert_bowtie_to_blast.pl	Fri Jul 25 05:57:27 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,126 +0,0 @@
-#!/usr/bin/perl 
-
-
-use warnings;
-use strict;
-use Getopt::Std;
-
-######################################### USAGE ################################
-
-my $usage=
-"$0 file_bowtie_result file_solexa_seq file_chromosome
-
-This is a converter which changes Bowtie output into Blast format.
-The input includes three files: a Bowtie result file (default Bowtie
-output file), a fasta file consisting of small Reads and a chromosome
-fasta file. It outputs the alignments in blast_parsed format.
-
-file_bowtie_result likes:
-
-AtFlower100010_x2	+	MIR319c	508	AAGGAGATTCTTTCAGTCCAG	IIIIIIIIIIIIIIIIIIIII	0	
-AtFlower1000188_x1	+	MIR2933a	421	TCGGAGAGGAAATTCGTCGGCG	IIIIIIIIIIIIIIIIIIIIII	0	
-
-file_solexa_seq likes:
-
->AtFlower100010_x2
-AAGGAGATTCTTTCAGTCCAG
-
-file_chromosome contains chromosome seq in fasta format
-
-";
-
-
-####################################### INPUT FILES ############################
-
-my $file_bowtie_result=shift or die $usage;
-my $file_short_seq=shift or die $usage;
-my $file_chromosome_seq=shift or die $usage;
-
-
-##################################### GLOBAL VARIBALES #########################
-
-my %short_seq_length=();
-my %chromosome_length=();
-
-
-######################################### MAIN ################################# 
-
-#get the short sequence id and its length
-sequence_length($file_short_seq,\%short_seq_length);
-
-#get the chromosome sequence id and its length
-sequence_length($file_chromosome_seq,\%chromosome_length);
-
-#convert bowtie result format to blast format;
-change_format($file_bowtie_result);
-
-exit;
-
-
-##################################### SUBROUTINES ##############################
-
-sub sequence_length{
-    my ($file,$hash) = @_;
-    my ($id, $desc, $sequence, $seq_length) = ();
-
-    open (FASTA, "<$file") or die "can not open $$file\n";
-    while (<FASTA>)
-    {
-        chomp;
-        if (/^>(\S+)(.*)/)
-	{
-	    $id       = $1;
-	    $desc     = $2;
-	    $sequence = "";
-	    while (<FASTA>){
-                chomp;
-                if (/^>(\S+)(.*)/){
-		    $$hash{$id}  = length $sequence;
-		    $id         = $1;
-		    $desc       = $2;
-		    $sequence   = "";
-		    next;
-                }
-		$sequence .= $_;
-            }
-        }
-    }
-    $seq_length=length($sequence);
-    $$hash{$id} = $seq_length;
-    close FASTA;
-}
-
-
-
-
-
-sub change_format{
-	#Change Bowtie format into blast format
-	my $file=shift @_;
-	open(FILE,"<$file")||die"can not open the bowtie result file:$!\n";
-  #open(BLASTOUT,">blastout")||die"can not create the blastout file:$!\n";
-	
-	while(<FILE>){
-		chomp;
-		my @tmp=split("\t",$_);
-	#Clean the reads ID
-		my @tmp1=split(" ",$tmp[0]);
-		print  "$tmp1[0]"."\t"."$short_seq_length{$tmp1[0]}"."\t"."1".'..'."$short_seq_length{$tmp1[0]}"."\t"."$tmp[2]"."\t"."$chromosome_length{$tmp[2]}"."\t";
-		if($tmp[1] eq "+"){
-			my $seq_end=$tmp[3] + $short_seq_length{$tmp1[0]};
-			my $seq_bg=$tmp[3] + 1;
-			print  "$seq_bg".'..'."$seq_end"."\t"."1e-04"."\t"."1.00"."\t"."42.1"."\t"."Plus / Plus"."\n";
-			}
-		if($tmp[1] eq "-"){
-			my $seq_end=$chromosome_length{$tmp[2]} - $tmp[3];
-			my $seq_bg=$seq_end - $short_seq_length{$tmp1[0]} + 1;
-			print  "$seq_bg".'..'."$seq_end"."\t"."1e-04"."\t"."1.00"."\t"."42.1"."\t"."Plus / Minus"."\n";
-			}
-		}
-	
-#	close BLASTOUT;
-
-}
-
-
-
diff -r 45de5e1ff487 -r 5691802f074b count_rfam_express.pl
--- a/count_rfam_express.pl	Fri Jul 25 05:57:27 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1800 +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;
-use File::Basename;
-
-my %opts;
-GetOptions(\%opts,"i=s","o=s","tag:s","h");
-if (!(defined $opts{i} and defined $opts{o} ) || defined $opts{h}) { #necessary arguments
-&usage;
-}
-
-my $filein=$opts{'i'};
-my $fileout=$opts{'o'};
-
-my $marks=defined $opts{'tag'} ? $opts{'tag'} : "";
-
-if(!(defined $opts{'tag'})){
-	my $line=`head -1 $filein`;
-	my @tmp=split/\t/,$line;
-	$tmp[0]=~/:([\d|_]+)_x(\d+)$/;
-	my @ss=split/_/,$1;
-	for (my $i=1;$i<=@ss;$i++) {
-		$marks .="Smp$i;";
-	}
-}
-
-my @marks=split/\;/,$marks;
-
-my %rfam_key;
-while(<DATA>){
-    chomp;
-    if(/^(\S+)\s+(\S+)$/){
-		$rfam_key{$1}=$2;
-    }
-}
-
-
-my %reads;
-my %tags;
-open IN,"<$filein";
-while (my $aline=<IN>) {
-	chomp $aline;
-	my @tmp=split/\t/,$aline;
-	$tmp[0]=~/:([\d|_]+)_x(\d+)$/;
-
-	my @exp=split/_/,$1;
-	my @tag=split/\;/,$tmp[2];
-
-	if (defined $rfam_key{$tag[0]}) {
-		for (my $i=0;$i<@exp;$i++) {
-			$reads{$rfam_key{$tag[0]}}[$i]+=$exp[$i];
-			$tags{$rfam_key{$tag[0]}}[$i]++ if($exp[$i]!=0);
-		}
-	}else{
-		for (my $i=0;$i<@exp;$i++) {
-			$reads{other}[$i]+=$exp[$i];
-			$tags{other}[$i]++ if($exp[$i]!=0);
-		}
-	}
-
-}
-close IN;
-
-$"="\t"; ##### @array print in \t
-open OUT,">$fileout";
-print OUT "####################################\n# small RNA expressed reads number #\n####################################\n";
-print OUT "#RNAname\t@marks\n";
-foreach my $key (keys %reads) {
-	print OUT $key;
-	for (my $i=0;$i<@{$reads{$key}} ;$i++) {
-		print OUT "\t",$reads{$key}[$i];
-	}
-	print OUT "\n";
-}
-
-print OUT "\n\n####################################\n# small RNA expressed tags number #\n####################################\n";
-print OUT "#RNAname\t@marks\n";
-
-foreach my $key (keys %tags) {
-	print OUT  $key;
-	for (my $i=0;$i<@{$reads{$key}} ;$i++) {
-		if(defined $tags{$key}[$i]){print OUT "\t",$tags{$key}[$i];}
-		else{print OUT "\t0";}
-	}
-	print OUT  "\n";
-}
-
-close OUT;
-$"=" "; ##### @array print in \t
-
-sub usage{
-print <<"USAGE";
-Version $version
-Usage:
-$0 -i -tag -o
-options:
--i input file# rfam bowtie bwt. format mapping result
--tag [string] sample marks# eg. sampleA;sampleB;sampleC
--o output file
-
--h help
-USAGE
-exit(1);
-}
-
-__DATA__
-RF00635	lncRNA
-RF01868	lncRNA
-RF01869	lncRNA
-RF01870	lncRNA
-RF01871	lncRNA
-RF01872	lncRNA
-RF01873	lncRNA
-RF01874	lncRNA
-RF01875	lncRNA
-RF01876	lncRNA
-RF01877	lncRNA
-RF01878	lncRNA
-RF01879	lncRNA
-RF01880	lncRNA
-RF01881	lncRNA
-RF01882	lncRNA
-RF01883	lncRNA
-RF01884	lncRNA
-RF01885	lncRNA
-RF01886	lncRNA
-RF01887	lncRNA
-RF01888	lncRNA
-RF01889	lncRNA
-RF01890	lncRNA
-RF01891	lncRNA
-RF01892	lncRNA
-RF01893	lncRNA
-RF01894	lncRNA
-RF01904	lncRNA
-RF01905	lncRNA
-RF01906	lncRNA
-RF01907	lncRNA
-RF01908	lncRNA
-RF01909	lncRNA
-RF01928	lncRNA
-RF01929	lncRNA
-RF01930	lncRNA
-RF01931	lncRNA
-RF01932	lncRNA
-RF01933	lncRNA
-RF01934	lncRNA
-RF01935	lncRNA
-RF01946	lncRNA
-RF01947	lncRNA
-RF01948	lncRNA
-RF01950	lncRNA
-RF01951	lncRNA
-RF01952	lncRNA
-RF01953	lncRNA
-RF01954	lncRNA
-RF01955	lncRNA
-RF01956	lncRNA
-RF01957	lncRNA
-RF01958	lncRNA
-RF01961	lncRNA
-RF01962	lncRNA
-RF01963	lncRNA
-RF01964	lncRNA
-RF01965	lncRNA
-RF01966	lncRNA
-RF01967	lncRNA
-RF01968	lncRNA
-RF01969	lncRNA
-RF01970	lncRNA
-RF01971	lncRNA
-RF01972	lncRNA
-RF01973	lncRNA
-RF01974	lncRNA
-RF01975	lncRNA
-RF01976	lncRNA
-RF01977	lncRNA
-RF01978	lncRNA
-RF01979	lncRNA
-RF01980	lncRNA
-RF01981	lncRNA
-RF01983	lncRNA
-RF01984	lncRNA
-RF01985	lncRNA
-RF01986	lncRNA
-RF01987	lncRNA
-RF01992	lncRNA
-RF02038	lncRNA
-RF02039	lncRNA
-RF02040	lncRNA
-RF02041	lncRNA
-RF02042	lncRNA
-RF02043	lncRNA
-RF02044	lncRNA
-RF02045	lncRNA
-RF02046	lncRNA
-RF02047	lncRNA
-RF02085	lncRNA
-RF02086	lncRNA
-RF02087	lncRNA
-RF02089	lncRNA
-RF02090	lncRNA
-RF02091	lncRNA
-RF02098	lncRNA
-RF02101	lncRNA
-RF02102	lncRNA
-RF02103	lncRNA
-RF02104	lncRNA
-RF02105	lncRNA
-RF02106	lncRNA
-RF02107	lncRNA
-RF02108	lncRNA
-RF02109	lncRNA
-RF02110	lncRNA
-RF02112	lncRNA
-RF02113	lncRNA
-RF02114	lncRNA
-RF02115	lncRNA
-RF02116	lncRNA
-RF02117	lncRNA
-RF02118	lncRNA
-RF02119	lncRNA
-RF02120	lncRNA
-RF02121	lncRNA
-RF02122	lncRNA
-RF02123	lncRNA
-RF02124	lncRNA
-RF02125	lncRNA
-RF02126	lncRNA
-RF02127	lncRNA
-RF02128	lncRNA
-RF02129	lncRNA
-RF02130	lncRNA
-RF02131	lncRNA
-RF02132	lncRNA
-RF02133	lncRNA
-RF02134	lncRNA
-RF02135	lncRNA
-RF02136	lncRNA
-RF02137	lncRNA
-RF02138	lncRNA
-RF02139	lncRNA
-RF02140	lncRNA
-RF02141	lncRNA
-RF02142	lncRNA
-RF02143	lncRNA
-RF02145	lncRNA
-RF02146	lncRNA
-RF02147	lncRNA
-RF02148	lncRNA
-RF02149	lncRNA
-RF02150	lncRNA
-RF02152	lncRNA
-RF02153	lncRNA
-RF02154	lncRNA
-RF02155	lncRNA
-RF02156	lncRNA
-RF02157	lncRNA
-RF02158	lncRNA
-RF02159	lncRNA
-RF02160	lncRNA
-RF02161	lncRNA
-RF02164	lncRNA
-RF02165	lncRNA
-RF02166	lncRNA
-RF02167	lncRNA
-RF02168	lncRNA
-RF02169	lncRNA
-RF02170	lncRNA
-RF02171	lncRNA
-RF02172	lncRNA
-RF02173	lncRNA
-RF02174	lncRNA
-RF02175	lncRNA
-RF02176	lncRNA
-RF02177	lncRNA
-RF02178	lncRNA
-RF02179	lncRNA
-RF02180	lncRNA
-RF02181	lncRNA
-RF02182	lncRNA
-RF02183	lncRNA
-RF02184	lncRNA
-RF02185	lncRNA
-RF02186	lncRNA
-RF02187	lncRNA
-RF02188	lncRNA
-RF02189	lncRNA
-RF02190	lncRNA
-RF02191	lncRNA
-RF02192	lncRNA
-RF02193	lncRNA
-RF02195	lncRNA
-RF02196	lncRNA
-RF02197	lncRNA
-RF02198	lncRNA
-RF02199	lncRNA
-RF02200	lncRNA
-RF02201	lncRNA
-RF02202	lncRNA
-RF02203	lncRNA
-RF02204	lncRNA
-RF02205	lncRNA
-RF02206	lncRNA
-RF02207	lncRNA
-RF02208	lncRNA
-RF02209	lncRNA
-RF02210	lncRNA
-RF02211	lncRNA
-RF02212	lncRNA
-RF02213	lncRNA
-RF02215	lncRNA
-RF02216	lncRNA
-RF02217	lncRNA
-RF02218	lncRNA
-RF02219	lncRNA
-RF02220	lncRNA
-RF02246	lncRNA
-RF02247	lncRNA
-RF02248	lncRNA
-RF02249	lncRNA
-RF02250	lncRNA
-RF02251	lncRNA
-RF02252	lncRNA
-RF02255	lncRNA
-RF02256	lncRNA
-RF02257	lncRNA
-RF02258	lncRNA
-RF02259	lncRNA
-RF02267	lncRNA
-RF02272	lncRNA
-RF00027	miRNA
-RF00047	miRNA
-RF00051	miRNA
-RF00052	miRNA
-RF00053	miRNA
-RF00073	miRNA
-RF00074	miRNA
-RF00075	miRNA
-RF00076	miRNA
-RF00103	miRNA
-RF00104	miRNA
-RF00129	miRNA
-RF00130	miRNA
-RF00131	miRNA
-RF00143	miRNA
-RF00144	miRNA
-RF00178	miRNA
-RF00237	miRNA
-RF00239	miRNA
-RF00241	miRNA
-RF00244	miRNA
-RF00245	miRNA
-RF00246	miRNA
-RF00247	miRNA
-RF00248	miRNA
-RF00249	miRNA
-RF00250	miRNA
-RF00251	miRNA
-RF00253	miRNA
-RF00254	miRNA
-RF00255	miRNA
-RF00256	miRNA
-RF00257	miRNA
-RF00258	miRNA
-RF00363	miRNA
-RF00364	miRNA
-RF00365	miRNA
-RF00366	miRNA
-RF00367	miRNA
-RF00445	miRNA
-RF00446	miRNA
-RF00451	miRNA
-RF00452	miRNA
-RF00455	miRNA
-RF00456	miRNA
-RF00464	miRNA
-RF00486	miRNA
-RF00637	miRNA
-RF00638	miRNA
-RF00639	miRNA
-RF00640	miRNA
-RF00641	miRNA
-RF00642	miRNA
-RF00643	miRNA
-RF00644	miRNA
-RF00645	miRNA
-RF00646	miRNA
-RF00647	miRNA
-RF00648	miRNA
-RF00649	miRNA
-RF00650	miRNA
-RF00651	miRNA
-RF00652	miRNA
-RF00653	miRNA
-RF00654	miRNA
-RF00655	miRNA
-RF00656	miRNA
-RF00657	miRNA
-RF00658	miRNA
-RF00659	miRNA
-RF00660	miRNA
-RF00661	miRNA
-RF00662	miRNA
-RF00663	miRNA
-RF00664	miRNA
-RF00665	miRNA
-RF00666	miRNA
-RF00667	miRNA
-RF00668	miRNA
-RF00669	miRNA
-RF00670	miRNA
-RF00671	miRNA
-RF00672	miRNA
-RF00673	miRNA
-RF00674	miRNA
-RF00675	miRNA
-RF00676	miRNA
-RF00677	miRNA
-RF00678	miRNA
-RF00679	miRNA
-RF00680	miRNA
-RF00681	miRNA
-RF00682	miRNA
-RF00683	miRNA
-RF00684	miRNA
-RF00685	miRNA
-RF00686	miRNA
-RF00687	miRNA
-RF00688	miRNA
-RF00689	miRNA
-RF00690	miRNA
-RF00691	miRNA
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-RF01302	snRNA
-RF01303	snRNA
-RF01304	snRNA
-RF01305	snRNA
-RF01306	snRNA
-RF01307	snRNA
-RF01308	snRNA
-RF01309	snRNA
-RF01310	snRNA
-RF01311	snRNA
-RF01312	snRNA
-RF01420	snRNA
-RF01421	snRNA
-RF01422	snRNA
-RF01423	snRNA
-RF01424	snRNA
-RF01425	snRNA
-RF01426	snRNA
-RF01427	snRNA
-RF01428	snRNA
-RF01429	snRNA
-RF01430	snRNA
-RF01431	snRNA
-RF01432	snRNA
-RF01433	snRNA
-RF01434	snRNA
-RF01435	snRNA
-RF01436	snRNA
-RF01437	snRNA
-RF01438	snRNA
-RF01439	snRNA
-RF01440	snRNA
-RF01441	snRNA
-RF01442	snRNA
-RF01443	snRNA
-RF01444	snRNA
-RF01445	snRNA
-RF01446	snRNA
-RF01447	snRNA
-RF01448	snRNA
-RF01449	snRNA
-RF01450	snRNA
-RF01451	snRNA
-RF01452	snRNA
-RF01498	snRNA
-RF01499	snRNA
-RF01500	snRNA
-RF01501	snRNA
-RF01505	snRNA
-RF01506	snRNA
-RF01507	snRNA
-RF01509	snRNA
-RF01511	snRNA
-RF01513	snRNA
-RF01514	snRNA
-RF01515	snRNA
-RF01516	snRNA
-RF01522	snRNA
-RF01523	snRNA
-RF01524	snRNA
-RF01525	snRNA
-RF01526	snRNA
-RF01531	snRNA
-RF01532	snRNA
-RF01533	snRNA
-RF01534	snRNA
-RF01535	snRNA
-RF01536	snRNA
-RF01537	snRNA
-RF01538	snRNA
-RF01539	snRNA
-RF01540	snRNA
-RF01541	snRNA
-RF01542	snRNA
-RF01543	snRNA
-RF01544	snRNA
-RF01545	snRNA
-RF01546	snRNA
-RF01547	snRNA
-RF01548	snRNA
-RF01549	snRNA
-RF01550	snRNA
-RF01551	snRNA
-RF01552	snRNA
-RF01553	snRNA
-RF01554	snRNA
-RF01555	snRNA
-RF01556	snRNA
-RF01557	snRNA
-RF01558	snRNA
-RF01559	snRNA
-RF01560	snRNA
-RF01561	snRNA
-RF01562	snRNA
-RF01563	snRNA
-RF01564	snRNA
-RF01565	snRNA
-RF01566	snRNA
-RF01567	snRNA
-RF01568	snRNA
-RF01569	snRNA
-RF01570	snRNA
-RF01572	snRNA
-RF01573	snRNA
-RF01574	snRNA
-RF01575	snRNA
-RF01576	snRNA
-RF01583	snRNA
-RF01584	snRNA
-RF01585	snRNA
-RF01586	snRNA
-RF01587	snRNA
-RF01588	snRNA
-RF01589	snRNA
-RF01590	snRNA
-RF01591	snRNA
-RF01592	snRNA
-RF01593	snRNA
-RF01594	snRNA
-RF01595	snRNA
-RF01596	snRNA
-RF01597	snRNA
-RF01598	snRNA
-RF01599	snRNA
-RF01600	snRNA
-RF01601	snRNA
-RF01602	snRNA
-RF01603	snRNA
-RF01604	snRNA
-RF01605	snRNA
-RF01606	snRNA
-RF01607	snRNA
-RF01608	snRNA
-RF01609	snRNA
-RF01610	snRNA
-RF01611	snRNA
-RF01612	snRNA
-RF01613	snRNA
-RF01614	snRNA
-RF01615	snRNA
-RF01617	snRNA
-RF01618	snRNA
-RF01620	snRNA
-RF01621	snRNA
-RF01622	snRNA
-RF01624	snRNA
-RF01625	snRNA
-RF01626	snRNA
-RF01627	snRNA
-RF01628	snRNA
-RF01629	snRNA
-RF01630	snRNA
-RF01631	snRNA
-RF01632	snRNA
-RF01633	snRNA
-RF01634	snRNA
-RF01635	snRNA
-RF01636	snRNA
-RF01637	snRNA
-RF01638	snRNA
-RF01639	snRNA
-RF01640	snRNA
-RF01641	snRNA
-RF01642	snRNA
-RF01644	snRNA
-RF01645	snRNA
-RF01646	snRNA
-RF01647	snRNA
-RF01648	snRNA
-RF01649	snRNA
-RF01650	snRNA
-RF01651	snRNA
-RF01652	snRNA
-RF01653	snRNA
-RF01654	snRNA
-RF01655	snRNA
-RF01658	snRNA
-RF01659	snRNA
-RF01660	snRNA
-RF01661	snRNA
-RF01662	snRNA
-RF01664	snRNA
-RF01802	snRNA
-RF01829	snRNA
-RF01844	snRNA
-RF01846	snRNA
-RF01847	snRNA
-RF01848	snRNA
-RF01860	snRNA
-RF01861	snRNA
-RF01862	snRNA
-RF01863	snRNA
-RF01864	snRNA
-RF01866	snRNA
-RF02163	snRNA
-RF00014	sRNA
-RF00018	sRNA
-RF00021	sRNA
-RF00034	sRNA
-RF00035	sRNA
-RF00057	sRNA
-RF00077	sRNA
-RF00078	sRNA
-RF00079	sRNA
-RF00081	sRNA
-RF00082	sRNA
-RF00083	sRNA
-RF00084	sRNA
-RF00101	sRNA
-RF00110	sRNA
-RF00111	sRNA
-RF00112	sRNA
-RF00113	sRNA
-RF00115	sRNA
-RF00116	sRNA
-RF00117	sRNA
-RF00118	sRNA
-RF00119	sRNA
-RF00121	sRNA
-RF00122	sRNA
-RF00124	sRNA
-RF00125	sRNA
-RF00126	sRNA
-RF00128	sRNA
-RF00166	sRNA
-RF00195	sRNA
-RF00368	sRNA
-RF00369	sRNA
-RF00370	sRNA
-RF00371	sRNA
-RF00372	sRNA
-RF00378	sRNA
-RF00444	sRNA
-RF00505	sRNA
-RF00519	sRNA
-RF00615	sRNA
-RF00616	sRNA
-RF01116	sRNA
-RF01385	sRNA
-RF01386	sRNA
-RF01387	sRNA
-RF01388	sRNA
-RF01389	sRNA
-RF01390	sRNA
-RF01391	sRNA
-RF01392	sRNA
-RF01393	sRNA
-RF01394	sRNA
-RF01395	sRNA
-RF01396	sRNA
-RF01397	sRNA
-RF01398	sRNA
-RF01399	sRNA
-RF01400	sRNA
-RF01401	sRNA
-RF01402	sRNA
-RF01403	sRNA
-RF01404	sRNA
-RF01405	sRNA
-RF01406	sRNA
-RF01407	sRNA
-RF01408	sRNA
-RF01409	sRNA
-RF01410	sRNA
-RF01411	sRNA
-RF01412	sRNA
-RF01457	sRNA
-RF01459	sRNA
-RF01460	sRNA
-RF01461	sRNA
-RF01462	sRNA
-RF01463	sRNA
-RF01464	sRNA
-RF01465	sRNA
-RF01466	sRNA
-RF01467	sRNA
-RF01468	sRNA
-RF01469	sRNA
-RF01470	sRNA
-RF01471	sRNA
-RF01472	sRNA
-RF01473	sRNA
-RF01474	sRNA
-RF01476	sRNA
-RF01477	sRNA
-RF01478	sRNA
-RF01479	sRNA
-RF01487	sRNA
-RF01488	sRNA
-RF01489	sRNA
-RF01492	sRNA
-RF01493	sRNA
-RF01494	sRNA
-RF01496	sRNA
-RF01503	sRNA
-RF01504	sRNA
-RF01512	sRNA
-RF01519	sRNA
-RF01520	sRNA
-RF01521	sRNA
-RF01527	sRNA
-RF01528	sRNA
-RF01529	sRNA
-RF01530	sRNA
-RF01571	sRNA
-RF01578	sRNA
-RF01579	sRNA
-RF01580	sRNA
-RF01581	sRNA
-RF01582	sRNA
-RF01619	sRNA
-RF01623	sRNA
-RF01643	sRNA
-RF01656	sRNA
-RF01663	sRNA
-RF01665	sRNA
-RF01668	sRNA
-RF01669	sRNA
-RF01670	sRNA
-RF01671	sRNA
-RF01672	sRNA
-RF01673	sRNA
-RF01674	sRNA
-RF01675	sRNA
-RF01676	sRNA
-RF01677	sRNA
-RF01678	sRNA
-RF01679	sRNA
-RF01680	sRNA
-RF01681	sRNA
-RF01682	sRNA
-RF01683	sRNA
-RF01684	sRNA
-RF01685	sRNA
-RF01686	sRNA
-RF01687	sRNA
-RF01690	sRNA
-RF01691	sRNA
-RF01693	sRNA
-RF01694	sRNA
-RF01696	sRNA
-RF01698	sRNA
-RF01699	sRNA
-RF01700	sRNA
-RF01701	sRNA
-RF01702	sRNA
-RF01703	sRNA
-RF01705	sRNA
-RF01706	sRNA
-RF01710	sRNA
-RF01712	sRNA
-RF01714	sRNA
-RF01718	sRNA
-RF01719	sRNA
-RF01722	sRNA
-RF01723	sRNA
-RF01728	sRNA
-RF01732	sRNA
-RF01742	sRNA
-RF01757	sRNA
-RF01762	sRNA
-RF01775	sRNA
-RF01781	sRNA
-RF01782	sRNA
-RF01783	sRNA
-RF01784	sRNA
-RF01789	sRNA
-RF01791	sRNA
-RF01793	sRNA
-RF01796	sRNA
-RF01808	sRNA
-RF01810	sRNA
-RF01812	sRNA
-RF01814	sRNA
-RF01815	sRNA
-RF01816	sRNA
-RF01817	sRNA
-RF01818	sRNA
-RF01819	sRNA
-RF01820	sRNA
-RF01821	sRNA
-RF01822	sRNA
-RF01823	sRNA
-RF01827	sRNA
-RF01828	sRNA
-RF01858	sRNA
-RF01867	sRNA
-RF02029	sRNA
-RF02030	sRNA
-RF02031	sRNA
-RF02049	sRNA
-RF02050	sRNA
-RF02051	sRNA
-RF02052	sRNA
-RF02053	sRNA
-RF02054	sRNA
-RF02055	sRNA
-RF02056	sRNA
-RF02057	sRNA
-RF02059	sRNA
-RF02060	sRNA
-RF02062	sRNA
-RF02063	sRNA
-RF02064	sRNA
-RF02065	sRNA
-RF02066	sRNA
-RF02067	sRNA
-RF02070	sRNA
-RF02071	sRNA
-RF02072	sRNA
-RF02073	sRNA
-RF02074	sRNA
-RF02075	sRNA
-RF02077	sRNA
-RF02078	sRNA
-RF02079	sRNA
-RF02080	sRNA
-RF02081	sRNA
-RF02082	sRNA
-RF02099	sRNA
-RF02100	sRNA
-RF02151	sRNA
-RF02221	sRNA
-RF02222	sRNA
-RF02223	sRNA
-RF02224	sRNA
-RF02225	sRNA
-RF02226	sRNA
-RF02227	sRNA
-RF02228	sRNA
-RF02230	sRNA
-RF02231	sRNA
-RF02232	sRNA
-RF02233	sRNA
-RF02234	sRNA
-RF02235	sRNA
-RF02236	sRNA
-RF02237	sRNA
-RF02238	sRNA
-RF02239	sRNA
-RF02240	sRNA
-RF02241	sRNA
-RF02242	sRNA
-RF02243	sRNA
-RF02268	sRNA
-RF02269	sRNA
-RF00127	sRNA
-RF01852	tRNA
-RF00005	tRNA
diff -r 45de5e1ff487 -r 5691802f074b filterReadsByLength.pl
--- a/filterReadsByLength.pl	Fri Jul 25 05:57:27 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,121 +0,0 @@
-#!/usr/bin/perl -w
-#Filename:
-#Author: Tian Dongmei
-#Email: tiandm@big.ac.cn
-#Date: 2010-01
-#Modified:
-#Description:  
-my $version=1.00;
-
-use strict;
-use Getopt::Long;
-use File::Basename;
-
-my %opts;
-GetOptions(\%opts,"i=s","min=i","max=i","o=s","mark:s","h");
-if (!(defined $opts{i} and defined $opts{o} and defined $opts{min} and defined $opts{max}) || defined $opts{h}) { #necessary arguments
-&usage;
-}
-
-my $mark=defined $opts{'mark'} ? $opts{'mark'} : "Sample";
-my @mark=split /,/,$mark;
-
-
-open OUT,">$opts{o}";
-open IN,"<$opts{i}";
-my %hash;my %reads;
-while (my $aline=<IN>) {
-	chomp $aline;
-	my $seq=<IN>;
-	chomp $seq;
-	
-	if($aline=~/:([\d|_]+)_x(\d+)$/){
-		my @ss=split/_/,$1;
-		for (my $i=0;$i<@ss;$i++) {
-			$hash{length($seq)}[$i]++ if($ss[$i]>0);
-			$hash{length($seq)}[$i] +=0 if($ss[$i]>0);
-			$reads{length($seq)}[$i]+=$ss[$i];
-		}
-	}
-	#else{$reads{length($seq)}+=1;}
-	if (length ($seq)>=$opts{'min'}  && length ($seq) <=$opts{'max'}) {
-		print OUT "$aline\n$seq\n";
-	}
-}
-close IN;
-close OUT;
-
-my $dir=dirname($opts{'o'});
-chdir $dir;
-my $lengthfile=$dir."/reads_length_distribution.txt";
-open OUT, ">$lengthfile";
-open R,">$dir/length_distribution.R";
-
-print OUT "Tags length\t@mark\n";
-
-my $samNo=@mark;
-my $avalue="";
-my @length=sort{$a<=>$b} keys %hash;
-foreach  (@length) {
-	print OUT $_,"\t@{$hash{$_}}\n";
-	my $vv=join ", ",@{$hash{$_}};
-	$avalue .="$vv,";
-}
-$avalue =~s/,$//;
-my $lengths=join ",",@length;
-my $marks=join "\",\"",@mark;
-
-print R  "a<-c($avalue)
-b<-matrix(a,ncol=$samNo,byrow=T)
-cl<-colors()
-names=c($lengths)
-legends=c(\"$marks\")
-png(\"Tags_length.png\",width=800,height=600)
-barplot(t(b),beside=TRUE,col=cl[1:$samNo],main=\"Tags Length Distribution\",names.arg=names,ylim=c(0,max(a)),legend.text=legends,args.legend=\"topleft\")
-abline(h=0)
-dev.off()
-
-";
-$avalue="";
-print OUT "\nReads length\t@mark\n";
-foreach  (@length) {
-	print OUT $_,"\t@{$reads{$_}}\n";
-	my $vv=join ", ", @{$reads{$_}};
-	$avalue .= "$vv,";
-}
-$avalue =~s/,$//;
-
-print R  "a<-c($avalue)\n
-b<-matrix(a,ncol=$samNo,byrow=T)
-
-png(\"Reads_length.png\",width=800,height=600)
-barplot(t(b),beside=TRUE,col=cl[1:$samNo],main=\"Reads Length Distribution\",names.arg=names,ylim=c(0,max(a)),legend.text=legends,args.legend=\"topleft\")
-abline(h=0)
-dev.off()
-
-";
-close OUT;
-close R;
-
-system ("R CMD BATCH $dir/length_distribution.R");
-
-#system ("rm $dir/length_distribution.R");
-#system ("rm $dir/length_distribution.Rout");
-#system ("rm $dir/.RData");
-sub usage{
-print <<"USAGE";
-Version $version
-Usage:
-$0 -i -o  -min -max -mark
-options:
-
--i input file
--o output file
--min reads min length.
--max reads max length.
--mark string #sample name eg: samA,samB,samC
--h help
-USAGE
-exit(1);
-}
-
diff -r 45de5e1ff487 -r 5691802f074b html.pl
--- a/html.pl	Fri Jul 25 05:57:27 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,269 +0,0 @@
-#!/usr/bin/perl -w
-#Filename:
-#Author: Tian Dongmei
-#Email: tiandm@big.ac.cn
-#Date: 2014-5-29
-#Modified:
-#Description: 
-my $version=1.00;
-
-use strict;
-use Getopt::Long;
-use File::Basename;
-
-my %opts;
-GetOptions(\%opts,"i=s","format=s","o=s","h");
-if (!(defined $opts{o} and defined $opts{format} and defined $opts{i} ) || defined $opts{h}) { #necessary arguments
-&usage;
-}
-my ($config,$prepath,$rfampath,$knownpath,$genomepath,$novelpath);
-my ($predir,$rfamdir,$knowndir,$genomedir,$noveldir);
-open IN,"<$opts{i}";
-$config=<IN>; chomp $config;
-$prepath=<IN>; chomp $prepath;
-$rfampath=<IN>;chomp $rfampath;
-$knownpath=<IN>; chomp $knownpath;
-$genomepath=<IN>; chomp $genomepath;
-$novelpath=<IN>; chomp $novelpath;
-close IN;
-my @tmp=split/\//,$prepath;
-$predir=$tmp[-1];
-@tmp=split/\//,$rfampath;
-$rfamdir=$tmp[-1];
-@tmp=split/\//,$knownpath;
-$knowndir=$tmp[-1];
-@tmp=split/\//,$genomepath;
-$genomedir=$tmp[-1];
-@tmp=split/\//,$novelpath;
-$noveldir=$tmp[-1];
-
-my $dir=dirname($opts{'o'});
-
-open OUT ,">$opts{'o'}";
-print OUT "<HTML>\n  <HEAD>\n  <TITLE> Analysis Report </TITLE>\n </HEAD>
- <BODY bgcolor=\"lightgray\">\n  <h1 align=\"center\">\n    <font face=\"黑体\">\n	<b>Small RNA Analysis Report</b>\n  </font>\n  </h1>
-  <h2>1. Sequence No. and quality</h2>
-  <h3>1.1 Sequece No.</h3>
-";
-
-### raw data no
-open IN,"<$config";
-my @files;my @marks; my @rawNo;
-while (my $aline=<IN>) {
-	chomp $aline;
-	my @tmp=split/\t/,$aline;
-	push @files,$tmp[0];
-	
-	my $no=`less $tmp[0] |wc -l `;
-	chomp $no;
-	if ($opts{'format'} eq "fq" || $opts{'format'} eq "fastq") {
-		$no=$no/4;
-	}
-	else{
-		$no=$no/2;
-	}
-	push @rawNo,$no;
-
-	push @marks,$tmp[1];
-}
-close IN;
-
-### preprocess 
-unless ($prepath=~/\/$/) {
-	$prepath .="/";
-}
-
-my @trimNo;my @collapse;
-my $collapsefile=$prepath."collapse_reads.fa";
-open IN,"<$collapsefile";
-while (my $aline=<IN>) {
-	chomp $aline;
-	<IN>;
-	$aline=~/:([\d|_]+)_x(\d+)$/;
-	my @lng=split/_/,$1;
-	for (my $i=0;$i<@lng;$i++) {
-		if ($lng[$i]>0) {
-			$trimNo[$i] +=$lng[$i];
-			$collapse[$i] ++;
-		}
-	}
-}
-close IN;
-
-my @cleanR;my @cleanT;
-my $clean=$prepath."collapse_reads_19_28.fa";
-open IN,"<$clean";
-while (my $aline=<IN>) {
-	chomp $aline;
-	<IN>;
-	$aline=~/:([\d|_]+)_x(\d+)$/;
-	my @lng=split/_/,$1;
-	for (my $i=0;$i<@lng;$i++) {
-		if ($lng[$i]>0) {
-			$cleanR[$i] +=$lng[$i];
-			$cleanT[$i] ++;
-		}
-	}
-}
-close IN;
-
-print OUT "<table border=\"1\">
-<tr align=\"center\">
-<th>&nbsp;</th>
-";
-foreach  (@marks) {
-	print OUT "<th> $_ </th>\n";
-}
-print  OUT "</tr>
-<tr align=\"center\">
-<th align=\"left\">Raw Reads No. </th>
-";
-foreach  (@rawNo) {
-	print OUT "<td> $_ </td>\n";
-}
-print OUT "</tr>
-<tr align=\"center\">
-<th align=\"left\">Reads No. After Trimed 3\' adapter </th>
-";
-foreach  (@trimNo) {
-	print OUT "<td> $_ </td>\n";
-}
-print OUT "</tr>
-<tr align=\"center\">
-<th align=\"left\">Unique Tags No. </th>
-";
-foreach  (@collapse) {
-	print OUT "<td> $_ </td>\n";
-}
-print OUT  "</tr>
-<tr align=\"center\">
-<th align=\"left\">Clean Reads No. </th>
-";
-foreach  (@cleanR) {
-	print OUT "<td> $_ </td>\n";
-}
-print OUT "</tr>
-<tr align=\"center\">
-<th align=\"left\">Clean Tags No. </th>
-";
-foreach  (@cleanT) {
-	print OUT "<td> $_ </td>\n";
-}
-print OUT "</tr>\n</table>";
-print OUT "<p>
-Note:<br />
-The raw data file path is: <b>$files[0]</b><br />
-";
-for (my $i=1;$i<@files;$i++) {
-	print OUT "&nbsp;&nbsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;<b>$files[$i]</b><br />";
-}
-print OUT "The collapsed file path is: <b>$collapsefile</b><br />
-The clean data file path is: <b>$clean</b><br />
-</p>
-<h2> 1. Sequence length count</h2>
-<h3> 1.1 Reads length</h3>
-";
-
-print OUT "<img src=\"./$predir/Reads_length.png\" alt=\"Reads_length.png\" width=\"400\" height=\"300\"/>
-<h3> 1.2 Tags length count</h3>
-<img src=\"./$predir/Tags_length.png\" alt=\"Tags_length.png\" width=\"400\" height=\"300\"/>
-<p> Note:<br />The sequence length data: <a href=\"./$predir/reads_length_distribution.txt\"> length file</a>
-</p>
-";
-
-#### rfam
-unless ($rfampath=~/\/$/) {
-	$rfampath .="/";
-}
-print OUT "<h2>2. Rfam non-miRNA annotation</h2>
-<h3>2.1 Reads count</h3>
-<table border=\"1\">
-<tr align=\"center\">
-";
-
-my @rfamR; my @rfamT;
-my $tag=1;
-open IN,"<$dir/rfam_non-miRNA_annotation.txt";
-while (my $aline=<IN>) {
-	chomp $aline;
-	$tag=0 if($aline=~/tags\s+number/);
-	next if($aline=~/^\#/);
-	next if($aline=~/^\s*$/);
-	my @tmp=split/\s+/,$aline;
-	if($tag == 1){push @rfamR,[@tmp];}
-	else{push @rfamT,[@tmp];}
-}
-close IN;
-
-
-print OUT "<th>RNA Name</th>\n";
-foreach  (@marks) {
-	print OUT "<th> $_ </th>\n";
-}
-for (my $i=0;$i<@rfamR;$i++) {
-	print  OUT "</tr>
-	<tr align=\"center\">
-	<th align=\"left\">$rfamR[$i][0]</th>
-	";
-	for (my $j=1;$j<@{$rfamR[$i]} ;$j++) {
-	print OUT "<td> $rfamR[$i][$j]</td>\n";
-	}
-}
-
-print OUT "</tr>\n</table>
-  <h3>2.2 Tags count</h3>
-  <table border=\"1\">
-   <tr align=\"center\">
-   <th>RNA Name</th>\n";
-foreach  (@marks) {
-	print OUT "<th> $_ </th>\n";
-}
-for (my $i=0;$i<@rfamT;$i++) {
-	print  OUT "</tr>
-	<tr align=\"center\">
-	<th align=\"left\">$rfamT[$i][0]</th>
-	";
-	for (my $j=1;$j<@{$rfamT[$i]} ;$j++) {
-	print OUT "<td> $rfamT[$i][$j]</td>\n";
-	}
-}
-print OUT "</tr>\n</table>
-<p>Note:<br />The rfam mapping results is: <b>$rfampath</b>";
-print OUT "<b>rfam_mapped.bwt</b></p>
-  <h2>3. MicroRNA result</h2>
-  <h3>3.1 known microRNA</h3>
-  <p>The known microRNA express list: <a href=\"./known_microRNA_express.txt\"> known_microRNA_express.txt</a><br/>
-  The known microRNA alngment file: <a href=\"./known_microRNA_express.aln\"> known_microRNA_express.aln</a><br/>
-  The known moRs file: <a href=\"./known_microRNA_express.moRs\"> known_microRNA_express.moRs</a><br/>
-  The known microRNA mature sequence file: <a href=\"./known_microRNA_mature.fa\"> known_microRNA_mature.fa</a><br/>
-  The knowm microRNA precursor sequence file: <a href=\"./known_microRNA_precursor.fa\"> known_microRNA_precursor.fa</a>
-  </p>
-
-  <h3>3.2 novel microRNA</h3>
-  <p>The novel microRNA prediction file:<a href=\"./microRNA_prediction.mrd\"> microRNA_prediction.mrd</a><br/>
-  The novel microRNA express list: <a href=\"./novel_microRNA_express.txt\"> novel_microRNA_express.txt</a><br/>
-  The novel microRNA mature sequence file: <a href=\"./novel_microRNA_mature.fa\"> novel_microRNA_mature.fa</a><br/>
-  The novel microRNA precursor sequence file: <a href=\"./novel_microRNA_precursor.fa\"> novel_microRNA_precursor.fa</a>
-  </p>
-";
-
-
-
-print OUT "
- </BODY>
-</HTML>
-";
-close OUT;
-
-sub usage{
-print <<"USAGE";
-Version $version
-Usage:
-$0 -o
-options:
--o output file
--h help
-USAGE
-exit(1);
-}
-
diff -r 45de5e1ff487 -r 5691802f074b miRNA_Express_and_sequence.pl
--- a/miRNA_Express_and_sequence.pl	Fri Jul 25 05:57:27 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,173 +0,0 @@
-#!/usr/bin/perl -w
-#Filename:
-#Author: Tian Dongmei
-#Email: tiandm@big.ac.cn
-#Date: 2014-6-4
-#Modified:
-#Description: solexa miRNA express and sequence
-my $version=1.00;
-
-use strict;
-use Getopt::Long;
-
-my %opts;
-GetOptions(\%opts,"i=s","list=s","fa=s","pre=s","tag=s","h");
-if (!(defined $opts{i} and defined $opts{list} and defined $opts{fa} and defined $opts{pre} and defined $opts{tag}) || defined $opts{h}) { #necessary arguments
-&usage;
-}
-
-my $filein=$opts{'i'};
-my $fileout=$opts{'list'};
-my $out=$opts{'fa'};
-my $preout=$opts{'pre'};
-
-=cut
-my %hash_pri;
-open PRI,"<$opts{p}";
-while (my $aline=<PRI>) {
-	chomp $aline;
-	if($aline=~/^>(\S+)/){$hash_pri{$1}=$aline;}
-}
-close PRI;
-=cut
-
-open IN,"<$filein"; #input file  
-open OUT,">$fileout"; #output file  
-open FA ,">$out";
-open PRE,">$preout";
-
-print OUT "#ID\tcoordinate\tpos1\tpos2";
-my @marks=split/\,/,$opts{'tag'};
-foreach  (@marks) {
-	print OUT "\t",$_,"_matureExp";
-}
-foreach  (@marks) {
-	print OUT "\t",$_,"_starExp";
-}
-foreach  (@marks) {
-	print OUT "\t",$_,"_totalExp";
-}
-
-print OUT "\n";
-
-my (%uniq_id,$novel);
-while (my $aline=<IN>) {
-	chomp $aline;
-	until ($aline =~ /^score\s+[-\d\.]+/){
-		$aline = <IN>;
-		if (eof) {last;}
-	}
-	if (eof) {last;}
-########## miRNA ID ################
-	$novel++;
-########### annotate####################
-	do {$aline=<IN>;} until($aline=~/flank_first_end/) ;
-	chomp $aline;
-	my @flank1=split/\t/,$aline;
-	do {$aline=<IN>;} until($aline=~/flank_second_beg/) ;
-	chomp $aline;
-	my @flank2=split/\t/,$aline;
-#		
-########## mature start loop pre ####
-	do {$aline=<IN>;} until($aline=~/mature_beg/) ;
-	chomp $aline;
-	my @start=split/\t/,$aline;
-#	$start[1] -=$flank1[1];
-	do {$aline=<IN>;} until($aline=~/mature_end/) ;
-	chomp $aline;
-	my @end=split/\t/,$aline;
-#	$end[1] -=$flank1[1];
-	do {$aline=<IN>;} until($aline=~/mature_seq/) ;
-	chomp $aline;
-	my @arr1=split/\t/,$aline;
-	do {$aline=<IN>;} until($aline=~/pre_seq/) ;
-	chomp $aline;
-	my @arr2=split/\t/,$aline;
-	do {$aline=<IN>;} until($aline=~/pri_id/) ;
-	chomp $aline;
-	my @pri_id=split/\t/,$aline;
-	do {$aline=<IN>;} until($aline=~/pri_seq/) ;
-	chomp $aline;
-	my @pri_seq=split/\t/,$aline;
-	do {$aline=<IN>;} until($aline=~/star_beg/) ;
-	chomp $aline;
-	my @star_start=split/\t/,$aline;
-#	$star_start[1] -=$flank1[1];
-	do {$aline=<IN>;} until($aline=~/star_end/) ;
-	chomp $aline;
-	my @star_end=split/\t/,$aline;
-#	$star_end[1] -=$flank1[1];
-	do {$aline=<IN>;} until($aline=~/star_seq/) ;
-	chomp $aline;
-	my @arr3=split/\t/,$aline;
-	print OUT "miR-c-$novel\t$pri_id[1]\tmature:$start[1]:$end[1]\tstar:$star_start[1]:$star_end[1]\t";
-	#print OUT "$arr1[1]\t$arr3[1]\t$arr2[1]\t\/\t";
-	print FA ">miR-c-$novel\n$arr1[1]\n";
-	print PRE ">miR-c-$novel\n$pri_seq[1]\n";
-########## reads count #############
-	<IN>;
-	my @count1;my @count2;my @count3;my @count4;
-	$aline=<IN>;
-	do {
-		chomp $aline;
-		my @reads=split/\t/,$aline;
-		my @pos=();
-		$reads[5]=~/(\d+)\.\.(\d+)/;
-#		$pos[0] =$1-$flank1[1];
-#		$pos[1] =$2-$flank1[1];
-		$pos[0]=$1;
-		$pos[1]=$2;
-		$reads[0]=~/:([\d|_]+)_x(\d+)$/;
-		my @ss=split/_/,$1;
-		for (my $i=0;$i<@ss ;$i++) {
-			if (!(defined $count3[$i])) {
-				$count3[$i]=0;
-			}
-			if (!(defined $count4[$i])) {
-				$count4[$i]=0;
-			}
-			$count2[$i]+=$ss[$i];
-
-		}
-#		$count3 +=$1 if($end[1]-$pos[0]>=10 && $pos[1]-$start[1]>=10 );
-#		$count4 +=$1 if($star_end[1]-$pos[0]>=10 && $pos[1]-$star_start[1]>=10 );
-#		$count1 =$1 if($end[1]-$pos[0]>=10 && $pos[1]-$start[1]>=10 && $count1<$1);
-#		$count2 =$1 if($star_end[1]-$pos[0]>=10 && $pos[1]-$star_start[1]>=10 && $count2<$1);
-		if($end[1]-$pos[1]>=-5 && $end[1]-$pos[1]<=5 && $pos[0]-$start[1]>=-3 && $pos[0]-$start[1]<=3 )
-		{
-			for (my $i=0;$i<@ss;$i++) {
-				$count3[$i]+=$ss[$i];
-			}
-		}
-		if($star_end[1]-$pos[1]<=5 && $star_end[1]-$pos[1]>=-5 && $pos[0]-$star_start[1]>=-3 && $pos[0]-$star_start[1]<=3){
-			for (my $i=0;$i<@ss;$i++) {
-				$count4[$i]+=$ss[$i];
-			}
-		} 
-		$aline=<IN>;
-		chomp $aline;
-	} until(length $aline < 1) ;
-	$"="\t";
-	print OUT "@count3\t@count4\t@count2\n";
-	$"=" ";
-}
-
-close IN;
-close OUT;
-
-sub usage{
-print <<"USAGE";
-Version $version
-Usage:
-$0 -i -list -fa -pre -tag
-options:
--i input file,predictions file
--list output file miRNA list file
--fa output file ,miRNA sequence fasta file.
--pre output file, miRNA precursor fasta file.
--tag string, sample names# eg: samA,samB,samC
--h help
-USAGE
-exit(1);
-}
-
diff -r 45de5e1ff487 -r 5691802f074b miRPlant.xml
--- a/miRPlant.xml	Fri Jul 25 05:57:27 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,90 +0,0 @@
-<tool id="plant_microRNA_v1" name="miRPlant" veision="1.0.0">
-  <description>tool for plant microRNA analisis</description>
-
-  <requirements>
-    <requirement type="set_environment">SCRIPT_PATH</requirement>
-    <requirement type="package" version="0.12.7">bowtie</requirement>
-    <requirement type="package" version="2.11.0">R</requirement>
-	<requirement type="package" version="0.0.13">fastx_toolkit </requirement>
-	<requirement type="package" version="1.5">ViennaRNA</requirement>
-  </requirements>
-
-  <!--command interpreter="perl">miPlant.pl -i $input -format $format -gfa $gfa -idx $index -pre $pre -mat $mat -rfam $rfam -idx2 $idx2 -D $D -a $a -M $M -min $min -max $max -mis $mis -e $e -f $f -v $v -r $r -dis $dis -flank $flank -mfe $mfe -t $t -o $output</command-->
-
-  <command interpreter="perl">miRPlant.pl 
-   ## Change this to accommodate the number of threads you have available.
-        -t \${GALAXY_SLOTS:-4}
-   ## Do or not delet rfam mapped tags
-    #if $params.delet_rfam == "yes":
-	-D 
-	#end if
-	-path \$SCRIPT_PATH
-
-    #for $j, $s in enumerate( $series )
-    ##rank_of_series=$j
-    -i ${s.input}
-    -tag ${s.tag}
-    #end for
-
-    -format $format -gfa $gfa -pre $pre -mat $mat -rfam $rfam  -a $a -M $mapnt -min $min -max $max -mis $mismatch -e $e -f $f -v $v -r $r -dis $dis -flank $flank -mfe $mfe
-  </command>
-
-  <inputs>
-
-   <repeat name="series" title="Series">
-     <param name="input" type="data" label="Raw data"/>
-     <param name="tag" type="text" data_ref="input" label="Sample name of raw data"/>
-   </repeat>
-
-	<conditional name="params">
-		<param name="delet_rfam" type="select" label="delet rfam mapped reads">
-		  <option value="yes" selected="true">yes</option>
-		  <option value="no">no</option>
-		 </param>
-    </conditional> <!-- params -->
-
-	<!--param name="input" format="tabular"  type="data" label="input config file" /-->
-	
-	<param name="format" type="select" lable="raw data format" multiple="false">
-	  <option value="fastq">Raw data is fastq. format</option>
-	  <option value="fasta">Raw data is fasta. format</option>
-	</param>
-	
-	<param name="gfa"  type="data" label="genome sequence fasta file"/>
-	<!--param type="data" name="index" label="genome sequence bowtie index"/-->
-	<param name="mat" type="data" label="mature microRNA sequence file" />
-	<param name="pre" type="data" label="precursor microRNA sequence fie" />
-	<param name="rfam" type="data" label="rfam sequence file" />
-	<!--param type="data" name="idx2" label="rfam sequence bowtie index " -->
-	<param name="a" type="text" value="ATCTCGTATG" label="3' adapter sequence" />
-	<param name="mapnt" type="integer" value="8" label="minimum adapter map nts" />
-	<param name="min" type="integer" value="19" label="minimum microRNA length" />
-	<param name="max" type="integer" value="28" label="maximum microRNA length" />
-	<param name="mismatch" type="integer" value="0" label="number of allowed mismatches when mapping reads to precursors" />
-	<param name="e" type="integer" value="2" label="number of nucleotides upstream of the mature sequence to consider" />
-	<param name="f" type="integer" value="5" label="number of nucleotides downstream of the mature sequence to consider" />
-	<param name="v" type="integer" value="0" label="report end-to-end hits less than v mismatches"/>
-	<param name="r" type="integer" value="25" label="a read is allowed to map up to this number of positions in the genome" />
-	<param name="dis" type="integer" value="200" label="Maximal space between miRNA and miRNA*" />
-	<param name="flank" type="integer" value="10" label="Flank sequence length of miRNA precursor" />
-	<param name="mfe" type="float" value="-30" label="Maximal free energy allowed for a miRNA precursor" />
-	<param name="thread" type="integer" value="1" label="number of threads" />
-  </inputs>
-
-  <outputs>
-   <data format="txt" name="known microRNA express list" from_work_dir="miRPlant_out/known_microRNA_express.txt"/>
-   <data format="txt" name="known microRNA express alignment" from_work_dir="miRPlant_out/known_microRNA_express.aln"/>
-   <data format="txt" name="known microRNA moRs result" from_work_dir="miRPlant_out/known_microRNA_express.moRs"/>
-   <data format="txt" name="known microRNA precursor file" from_work_dir="miRPlant_out/known_microRNA_precursor.fa"/>
-   <data format="txt" name="known microRNA mature file" from_work_dir="miRPlant_out/known_microRNA_mature.fa"/>
-   <data format="txt" name="novel microRNA prediction file" from_work_dir="miRPlant_out/known_microRNA_mature.fa"/>
-   <data format="txt" name="novel microRNA express list" from_work_dir="miRPlant_out/novel_microRNA_express.txt"/>
-   <data format="txt" name="novel microRNA precursor file" from_work_dir="miRPlant_out/novel_microRNA_precursor.fa"/>
-   <data format="txt" name="novel microRNA mature sequence file" from_work_dir="miRPlant_out/novel_microRNA_mature.fa"/>
-   <data format="txt" name="analysis result" from_work_dir="miRPlant_out/result.html"/>
-  </outputs>
-
- <help>
-
- </help>
- </tool>
diff -r 45de5e1ff487 -r 5691802f074b precursors.pl
--- a/precursors.pl	Fri Jul 25 05:57:27 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,789 +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;
-use RNA;
-
-my %opts;
-GetOptions(\%opts,"map=s","g=s","d:i","f:i","o=s","e:f","s=s","h");
-if (!(defined $opts{map} and defined $opts{g} and defined $opts{o} and defined $opts{s} ) || defined $opts{h}) { #necessary arguments
-&usage;
-}
-
-my $filein=$opts{'map'};
-my $faout=$opts{'o'};
-my $strout=$opts{'s'};
-my $genome= $opts{'g'};
-
-my $maxd=defined $opts{'d'} ? $opts{'d'} : 200;
-my $flank=defined $opts{'f'}? $opts{'f'} : 10;
-
-my $MAX_ENERGY=-18;
-if (defined $opts{'e'}) {$MAX_ENERGY=$opts{'e'};}
-my $MAX_UNPAIR=5;
-my $MIN_PAIR=15;
-my $MAX_SIZEDIFF=4;
-my $MAX_BULGE=2;
-my $ASYMMETRY=5;
-my $MIN_UNPAIR=0;
-my $MIN_SPACE=5;
-my $MAX_SPACE=$maxd;
-my $FLANK=$flank;
-
-######### load in genome sequences start ########
-my %genome;
-my %lng;
-my $name;
-open IN,"<$genome";
-while (my $aline=<IN>) {
-	chomp $aline;
-	next if($aline=~/^\#/);
-	if ($aline=~/^>(\S+)/) {
-		$name=$1;
-		next;
-	}
-	$genome{$name} .=$aline;
-}
-close IN;
-foreach my $key (keys %genome) {
-	$lng{$key}=length($genome{$key});
-}
-####### load in genome sequences end ##########
-
-my %breaks; ### reads number bigger than 3
-open IN,"<$filein"; #input file  
-while (my $aline=<IN>) {
-	chomp $aline;
-	my @tmp=split/\t/,$aline;
-	$tmp[0]=~/_x(\d+)$/;
-	my $no=$1;
-	next if($no<3);
-	#my $trand=&find_strand($tmp[9]);
-	#my @pos=split/\.\./,$tmp[5];
-	my $end=$tmp[3]+length($tmp[4])-1;
-	if($tmp[1] eq "-"){$tmp[4]=revcom($tmp[4]);}
-	push @{$breaks{$tmp[2]}{$tmp[1]}},[$tmp[3],$end,$no,$tmp[4]]; ### 0 base
-}
-close IN;
-
-my %cites; ### peaks
-foreach my $chr (keys %breaks) {
-	foreach my $strand (keys %{$breaks{$chr}}) {
-		my @array=@{$breaks{$chr}{$strand}};
-		@array=sort{$a->[0]<=>$b->[0]} @array;
-		for (my $i=0;$i<@array;$i++) {
-			my $start=$array[$i][0];my $end=$array[$i][1];
-			my @subarray=();
-			push @subarray,$array[$i];
-
-			for (my $j=$i+1;$j<@array;$j++) {
-				if ($start<$array[$j][1] && $end>$array[$j][0]) {
-					push @subarray,$array[$j];
-					($start,$end)=&newpos($start,$end,$array[$j][0],$array[$j][1]);
-				}
-				else{
-					$i=$j;
-					&find_cites(\@subarray,$chr,$strand);
-					last;
-				}
-			}
-		}
-	}
-}
-
-open FA,">$faout"; #output file 
-open STR,">$strout";
-foreach my $chr (keys %cites) {
-	foreach my $strand (keys %{$cites{$chr}}) {
-
-		my @array2=@{$cites{$chr}{$strand}};
-		@array2=sort{$a->[0]<=>$b->[0]} @array2;
-		&excise(\@array2,$chr,$strand);
-	}
-}
-close FA;
-close STR;
-sub oneCiteDn{
-	my ($array,$a,$chr,$strand)=@_;
-
-	my $ss=$$array[$a][0]-$flank;
-	$ss=0 if($ss<0);
-	my $ee=$$array[$a][1]+$maxd+$flank;
-	$ee=$lng{$chr} if($ee>$lng{$chr});
-	
-	my $seq=substr($genome{$chr},$ss,$ee-$ss+1);
-	if($strand eq "-"){$seq=revcom($seq);}
-
-	my $val=&ffw1($seq,$$array[$a][3],$chr,$strand,$ss,$ee);
-	return $val;
-}
-sub oneCiteUp{
-	my ($array,$a,$chr,$strand)=@_;
-
-	my $ss=$$array[$a][0]-$maxd-$flank;
-	$ss=0 if($ss<0);
-	my $ee=$$array[$a][1]+$flank;
-	$ee=$lng{$chr} if($ee>$lng{$chr});
-	
-	my $seq=substr($genome{$chr},$ss,$ee-$ss+1);
-	if($strand eq "-"){$seq=revcom($seq);}
-
-	my $val=&ffw1($seq,$$array[$a][3],$chr,$strand,$ss,$ee);
-	return $val;
-
-}
-
-sub twoCites{
-	my ($array,$a,$b,$chr,$strand)=@_;
-
-	my $ss=$$array[$a][0]-$flank;
-	$ss=0 if($ss<0);
-	my $ee=$$array[$b][1]+$flank;
-	$ee=$lng{$chr} if($ee>$lng{$chr});
-	
-	my $seq=substr($genome{$chr},$ss,$ee-$ss+1);
-	if($strand eq "-"){$seq=revcom($seq);}
-
-#	my( $str,$mfe)=RNA::fold($seq);
-#	return 0 if($mfe>$MAX_ENERGY); ### minimum mfe
-	my $val=&ffw2($seq,$$array[$a][3],$$array[$b][3],$chr,$strand,$ss,$ee);
-	
-	return $val;
-
-}
-sub excise{
-	my ($cluster,$chr,$strand)=@_;
-
-	my $last_pos=0;
-	for (my $i=0;$i<@{$cluster};$i++) {
-		next if($$cluster[$i][0]<$last_pos);
-		my $ok=0;
-		for (my $j=$i+1;$j<@{$cluster} ;$j++) {
-			if($$cluster[$j][0]-$$cluster[$i][1]>$maxd){
-				$i=$j;
-				last;
-			}else{
-				$ok=&twoCites($cluster,$i,$j,$chr,$strand);
-				if($ok){ $last_pos=$$cluster[$j][1]+$flank; $i=$j; last;}
-			}
-		}
-		next if($ok);
-
-		$ok=&oneCiteDn($cluster,$i,$chr,$strand);
-		if($ok){$last_pos=$$cluster[$i][1]+$maxd+$flank; next;}
-		$ok=&oneCiteUp($cluster,$i,$chr,$strand);
-		if($ok){$last_pos=$$cluster[$i][1]+$flank;next;}
-	}
-
-
-}
-
-sub ffw2{
-	my ($seq,$tag1,$tag2,$chr,$strand,$ss,$ee)=@_;
-	
-	my $N_count=$seq=~tr/N//;  ## precursor sequence has not more than 5 Ns
-	if ($N_count > 5) {
-		return 0;
-	}
-
-	my $seq_length=length $seq;
-	# position tag1 and tag2
-	my $tag1_beg=index($seq,$tag1,0)+1;
-	if ($tag1_beg < 1) {
-		warn "[ffw2] coordinate error.\n";
-#		$fold->{reason}="coordinate error";
-		return 0;
-	}
-	my $tag2_beg=index($seq,$tag2,0)+1;
-	if ($tag2_beg < 1) {
-		warn "[ffw2] coordinate error.\n";
-#		$fold->{reason}="coordinate error";
-		return 0;
-	}
-	if ($tag2_beg < $tag1_beg) {
-		# swap tag1 and tag2
-		($tag1,$tag2)=($tag2,$tag1);
-		($tag1_beg,$tag2_beg)=($tag2_beg,$tag1_beg);
-	}
-	my $tag1_end=$tag1_beg+length($tag1)-1;
-	my $tag2_end=$tag2_beg+length($tag2)-1;
-	# re-clipping
-	my $beg=$tag1_beg-$FLANK; $beg=1 if $beg < 1;
-	my $end=$tag2_end+$FLANK; $end=$seq_length if $end > $seq_length;
-	$seq=substr($seq,$beg-1,$end-$beg+1);
-	$seq_length=length $seq;
-	# re-reposition
-	$tag1_beg=index($seq,$tag1,0)+1;
-	if ($tag1_beg < 1) {
-		warn "[ffw2] coordinate error.\n";
-#		$fold->{reason}="coordinate error";
-		return 0;
-	}
-	
-	$tag2_beg=index($seq,$tag2,0)+1;
-	if ($tag2_beg < 1) {
-		warn "[ffw2] coordinate error.\n";
-#		$fold->{reason}="coordinate error";
-		return 0;
-	}
-	$tag1_end=$tag1_beg+length($tag1)-1;
-	$tag2_end=$tag2_beg+length($tag2)-1;
-
-	# fold
-	my ($struct,$mfe)=RNA::fold($seq);
-	$mfe=sprintf "%.2f", $mfe;
-	if ($mfe > $MAX_ENERGY) {return 0;}
-
-	# tag1
-	my $tag1_length=$tag1_end-$tag1_beg+1;
-	my $tag1_struct=substr($struct,$tag1_beg-1,$tag1_length);
-	my $tag1_arm=which_arm($tag1_struct);
-	my $tag1_unpair=$tag1_struct=~tr/.//;
-	my $tag1_pair=$tag1_length-$tag1_unpair;
-	my $tag1_max_bulge=biggest_bulge($tag1_struct);
-	if ($tag1_arm ne "5p") { return 0;} # tag not in stem
-#	if ($tag1_unpair > $MAX_UNPAIR) {$fold->{reason}="unpair=$tag1_unpair ($MAX_UNPAIR)"; return $pass}
-	if ($tag1_pair < $MIN_PAIR) {return 0;}
-	if ($tag1_max_bulge > $MAX_BULGE) {return 0;}
-
-	# tag2
-	my $tag2_length=$tag2_end-$tag2_beg+1;
-	my $tag2_struct=substr($struct,$tag2_beg-1,$tag2_length);
-	my $tag2_arm=which_arm($tag2_struct);
-	my $tag2_unpair=$tag2_struct=~tr/.//;
-	my $tag2_pair=$tag2_length-$tag2_unpair;
-	my $tag2_max_bulge=biggest_bulge($tag2_struct);
-	if ($tag2_arm ne "3p") {return 0;} # star not in stem
-#	if ($tag2_unpair > $MAX_UNPAIR) {$fold->{reason}="unpair=$tag2_unpair ($MAX_UNPAIR)"; return $pass}
-	if ($tag2_pair < $MIN_PAIR) {return 0;}
-	if ($tag2_max_bulge > $MAX_BULGE) {return 0;}
-
-	# space size between miR and miR*
-	my $space=$tag2_beg-$tag1_end-1;
-	if ($space < $MIN_SPACE) {return 0;}
-	if ($space > $MAX_SPACE) {return 0;}
-	
-	# size diff of miR and miR*
-	my $size_diff=abs($tag1_length-$tag2_length);
-	if ($size_diff > $MAX_SIZEDIFF) {return 0;}
-
-	# build base pairing table
-	my %pairtable;
-	&parse_struct($struct,\%pairtable); # coords count from 1
-
-	my $asy1=get_asy(\%pairtable,$tag1_beg,$tag1_end);
-	my $asy2=get_asy(\%pairtable,$tag2_beg,$tag2_end);
-	my $asy=($asy1 < $asy2) ? $asy1 : $asy2;
-	if ($asy > $ASYMMETRY) {return 0}
-
-	# duplex fold, determine whether two matures like a miR/miR* ike duplex
-	my ($like_mir_duplex1,$duplex_pair,$overhang1,$overhang2)=likeMirDuplex1($tag1,$tag2);
-	# parse hairpin, determine whether two matures form miR/miR* duplex in hairpin context
-	my ($like_mir_duplex2,$duplex_pair2,$overhang_b,$overhang_t)=likeMirDuplex2(\%pairtable,$tag1_beg,$tag1_end,$tag2_beg,$tag2_end);
-	if ($like_mir_duplex1==0 && $like_mir_duplex2==0) {
-		return 0;
-	}
-
-	print FA ">$chr:$strand:$ss..$ee\n$seq\n";
-	print STR ">$chr:$strand:$ss..$ee\n$seq\n$struct\t($mfe)\n";
-	
-	return 1;	
-}
-
-sub ffw1{
-	my ($seq,$tag,$chr,$strand,$ss,$ee)=@_;
-	my $pass=0;
-
-	my $N_count=$seq=~tr/N//;
-	if ($N_count > 5) {
-		return 0;
-	}
-
-	my $seq_length=length $seq;
-	my $tag_length=length $tag;
-
-	# position
-	my $tag_beg=index($seq,$tag,0)+1;
-	if ($tag_beg < 1) {
-		 warn "[ffw1] coordinate error.\n";
-		 return $pass;
-	}
-	my $tag_end=$tag_beg+length($tag)-1;
-	
-	
-	# define candidate precursor by hybrid short arm to long arm, not solid enough
-	my($beg,$end)=define_precursor($seq,$tag);
-	if (not defined $beg) {
-		return $pass;
-	}
-	if (not defined $end) {
-		return $pass;
-	}
-	$seq=substr($seq,$beg-1,$end-$beg+1);
-	$seq_length=length $seq;
-	
-	
-	# fold
-	my ($struct,$mfe)=RNA::fold($seq);
-	$mfe=sprintf "%.2f",$mfe;
-	if ($mfe > $MAX_ENERGY) {
-		$pass=0;
-		return $pass;
-	}
-
-	# reposition
-	$tag_beg=index($seq,$tag,0)+1;
-	if ($tag_beg < 1) {
-		 warn "[ffw1] coordinate error.\n";
-		 return 0;
-	}
-	$tag_end=$tag_beg+length($tag)-1;
-
-	my $tag_struct=substr($struct,$tag_beg-1,$tag_length);
-	my $tag_arm=which_arm($tag_struct);
-	my $tag_unpair=$tag_struct=~tr/.//;
-	my $tag_pair=$tag_length-$tag_unpair;
-	my $tag_max_bulge=biggest_bulge($tag_struct);
-	if ($tag_arm eq "-") { return $pass;}
-#	if ($tag_unpair > $MAX_UNPAIR) {$fold->{reason}="unpair=$tag_unpair ($MAX_UNPAIR)"; return $pass}
-	if ($tag_pair < $MIN_PAIR) { return $pass;}
-	if ($tag_max_bulge > $MAX_BULGE) {return $pass;}
-
-	# build base pairing table
-	my %pairtable;
-	&parse_struct($struct,\%pairtable); # coords count from 1
-	
-	# get star
-	my ($star_beg,$star_end)=get_star(\%pairtable,$tag_beg,$tag_end);
-	my $star=substr($seq,$star_beg-1,$star_end-$star_beg+1);
-	my $star_length=$star_end-$star_beg+1;
-	my $star_struct=substr($struct,$star_beg-1,$star_end-$star_beg+1);
-	my $star_arm=which_arm($star_struct);
-	my $star_unpair=$star_struct=~tr/.//;
-	my $star_pair=$star_length-$star_unpair;
-	my $star_max_bulge=biggest_bulge($star_struct);
-	if ($star_arm eq "-") { return $pass;}
-#	if ($star_unpair > $MAX_UNPAIR) {$fold->{reason}="unpair=$star_unpair ($MAX_UNPAIR)"; return $pass}
-	if ($star_pair < $MIN_PAIR) {return $pass;}
-	if ($star_max_bulge > $MAX_BULGE) {return $pass;}
-
-	if ($tag_arm eq $star_arm) {return $pass;}
-	
-	# space size between miR and miR*
-	my $space;
-	if ($tag_beg < $star_beg) {
-		$space=$star_beg-$tag_end-1;
-	}
-	else {
-		$space=$tag_beg-$star_end-1;
-	}
-	if ($space < $MIN_SPACE) { return $pass;}
-	if ($space > $MAX_SPACE) { return $pass;}
-
-	# size diff
-	my $size_diff=abs($tag_length-$star_length);
-	if ($size_diff > $MAX_SIZEDIFF) { return $pass;}
-	
-	# asymmetry
-	my $asy=get_asy(\%pairtable,$tag_beg,$tag_end);
-	if ($asy > $ASYMMETRY) {return $pass;}
-	
-	$pass=1;
-	print FA ">$chr:$strand:$ss..$ee\n$seq\n";
-	print STR ">$chr:$strand:$ss..$ee\n$seq\n$struct\t($mfe)\n";
-	return $pass;
-
-}
-sub get_star {
-	my($table,$beg,$end)=@_;
-	
-	my ($s1,$e1,$s2,$e2); # s1 pair to s2, e1 pair to e2
-	foreach my $i ($beg..$end) {
-		if (defined $table->{$i}) {
-			my $j=$table->{$i};
-			$s1=$i;
-			$s2=$j;
-			last;
-		}
-	}
-	foreach my $i (reverse ($beg..$end)) {
-		if (defined $table->{$i}) {
-			my $j=$table->{$i};
-			$e1=$i;
-			$e2=$j;
-			last;
-		}
-	}
-#	print "$s1,$e1 $s2,$e2\n";
-	
-	# correct terminus
-	my $off1=$s1-$beg;
-	my $off2=$end-$e1;
-	$s2+=$off1;
-	$s2+=2; # 081009
-	$e2-=$off2; $e2=1 if $e2 < 1;
-	$e2+=2; $e2=1 if $e2 < 1; # 081009
-	($s2,$e2)=($e2,$s2) if ($s2 > $e2);
-	return ($s2,$e2);
-}
-
-sub define_precursor {
-	my $seq=shift;
-	my $tag=shift;
-
-	my $seq_length=length $seq;
-	my $tag_length=length $tag;
-	my $tag_beg=index($seq,$tag,0)+1;
-	my $tag_end=$tag_beg+$tag_length-1;
-
-	# split the candidate region into short arm and long arm
-	my $tag_arm;
-        my ($larm,$larm_beg,$larm_end);
-	my ($sarm,$sarm_beg,$sarm_end);
-        if ($tag_beg-1 < $seq_length-$tag_end) { # on 5' arm
-                $sarm=substr($seq,0,$tag_end);
-		$larm=substr($seq,$tag_end);
-		$sarm_beg=1;
-		$sarm_end=$tag_end;
-		$larm_beg=$tag_end+1;
-		$larm_end=$seq_length;
-		$tag_arm="5p";
-        }
-        else {
-            $larm=substr($seq,0,$tag_beg-1); # on 3' arm
-			$sarm=substr($seq,$tag_beg-1);
-			$larm_beg=1;
-			$larm_end=$tag_beg-1;
-			$sarm_beg=$tag_beg;
-			$sarm_end=$seq_length;
-			$tag_arm="3p";
-        }
-	
-#	print "$sarm_beg,$sarm_end $sarm\n";
-#	print "$larm_beg,$larm_end $larm\n";
-
-	# clipping short arm
-	if ($tag_arm eq "5p") {
-		$sarm_beg=$tag_beg-$flank; $sarm_beg=1 if $sarm_beg < 1;
-		$sarm=substr($seq,$sarm_beg-1,$sarm_end-$sarm_beg+1);
-	}
-	else {
-		$sarm_end=$tag_end+$flank; $sarm_end=$seq_length if $sarm_end > $seq_length;
-		$sarm=substr($seq,$sarm_beg-1,$sarm_end-$sarm_beg+1);
-	}
-#	print "$sarm_beg,$sarm_end $sarm\n";
-#	print "$larm_beg,$larm_end $larm\n";
-
-	# define the precursor by hybriding short arm to long arm
-	my $duplex=RNA::duplexfold($sarm,$larm);
-	my $struct=$duplex->{structure};
-	my $energy=sprintf "%.2f", $duplex->{energy};
-	my ($str1,$str2)=split(/&/,$struct);
-	my $pair=$str1=~tr/(//;
-#	print "pair=$pair\n";
-	my $beg1=$duplex->{i}+1-length($str1);
-	my $end1=$duplex->{i};
-	my $beg2=$duplex->{j};
-	my $end2=$duplex->{j}+length($str2)-1;
-#	print "$beg1:$end1 $beg2:$end2\n";
-	# transform coordinates
-	$beg1=$beg1+$sarm_beg-1;
-	$end1=$end1+$sarm_beg-1;
-	$beg2=$beg2+$larm_beg-1;
-	$end2=$end2+$larm_beg-1;
-#	print "$beg1:$end1 $beg2:$end2\n";
-	
-	my $off5p=$beg1-$sarm_beg;
-	my $off3p=$sarm_end-$end1;
-	$beg2-=$off3p; $beg2=1 if $beg2 < 1;
-	$end2+=$off5p; $end2=$seq_length if $end2 > $seq_length;
-
-#	print "$beg1:$end1 $beg2:$end2\n";
-	
-	my $beg=$sarm_beg < $beg2 ? $sarm_beg : $beg2;
-	my $end=$sarm_end > $end2 ? $sarm_end : $end2;
-	
-	return if $pair < $MIN_PAIR;
-#	print "$beg,$end\n";
-	return ($beg,$end);
-}
-
-
-# duplex fold, judge whether two short seqs like a miRNA/miRNA* duplex
-sub likeMirDuplex1 {
-	my $seq1=shift;
-	my $seq2=shift;
-	my $like_mir_duplex=1;
-	
-	my $length1=length $seq1;
-	my $length2=length $seq2;
-	my $duplex=RNA::duplexfold($seq1, $seq2);
-	my $duplex_struct=$duplex->{structure};
-	my $duplex_energy=sprintf "%.2f", $duplex->{energy};
-	my ($str1,$str2)=split(/&/,$duplex_struct);
-	my $beg1=$duplex->{i}+1-length($str1);
-	my $end1=$duplex->{i};
-	my $beg2=$duplex->{j};
-	my $end2=$duplex->{j}+length($str2)-1;
-	
-	# revise beg1, end1, beg2, end2
-	$str1=~/^(\.*)/;
-	$beg1+=length($1);
-	$str1=~/(\.*)$/;
-	$end1-=length($1);
-	$str2=~/^(\.*)/;
-	$beg2+=length($1);
-	$str2=~/(\.*)$/;
-	$end2-=length($1);
-
-	my $pair_num=$str1=~tr/(//;
-	my $overhang1=($length2-$end2)-($beg1-1); # 3' overhang at hairpin bottom
-	my $overhang2=($length1-$end1)-($beg2-1); # 3' overhang at hairpin neck
-#	print $pair_num,"\n";
-#	print $overhang1,"\n";
-#	print $overhang2,"\n";
-	if ($pair_num < 13) {
-		$like_mir_duplex=0;
-	}
-	if ($overhang1 < 0 || $overhang2 < 0 ) {
-		$like_mir_duplex=0;
-	}
-	if ($overhang1 > 4 || $overhang2 > 4) {
-		$like_mir_duplex=0;
-	}
-	return ($like_mir_duplex,$pair_num,$overhang1,$overhang2);
-}
-
-# judge whether two matures form miR/miR* duplex, in hairpin context
-sub likeMirDuplex2 {
-	my ($table,$beg1,$end1,$beg2,$end2)=@_;
-	my $like_mir_duplex=1;
-
-#	   s1         e1
-#   5 ----------------------------3	
-#      | | |||| |||               |
-#3 -------------------------------5
-#      e2         s2
-
-	my $pair_num=0;
-	my $overhang1=0;
-	my $overhang2=0;
-	my ($s1,$e1,$s2,$e2);
-	foreach my $i ($beg1..$end1) {
-		if (defined $table->{$i}) {
-			my $j=$table->{$i};
-			if ($j <= $end2 && $j >= $beg2) {
-				$s1=$i;
-				$e2=$j;
-				last;
-			}
-		}
-	}
-	foreach my $i (reverse ($beg1..$end1)) {
-		if (defined $table->{$i}) {
-			my $j=$table->{$i};
-			if ($j <= $end2 && $j >= $beg2) {
-				$e1=$i;
-				$s2=$j;
-				last;
-			}
-		}
-	}
-
-#	print "$beg1,$end1 $s1,$e1\n";
-#	print "$beg2,$end2 $s2,$e2\n";
-
-	foreach my $i ($beg1..$end1) {
-		if (defined $table->{$i}) {
-			my $j=$table->{$i};
-			if ($j <= $end2 && $j >= $beg2) {
-				++$pair_num;
-			}
-		}
-	}
-	if (defined $s1 && defined $e2) {
-		$overhang1=($end2-$e2)-($s1-$beg1);
-	}
-	if (defined $e1 && defined $s2) {
-		$overhang2=($end1-$e1)-($s2-$beg2);
-	}
-	
-	if ($pair_num < 13) {
-		$like_mir_duplex=0;
-	}
-	if ($overhang1 < 0 && $overhang2 < 0) {
-		$like_mir_duplex=0;
-	}
-	return ($like_mir_duplex,$pair_num,$overhang1,$overhang2);
-}
-sub parse_struct {
-	my $struct=shift;
-	my $table=shift;
-
-	my @t=split('',$struct);
-	my @lbs; # left brackets
-	foreach my $k (0..$#t) {
-		if ($t[$k] eq "(") {
-			push @lbs, $k+1;
-		}
-		elsif ($t[$k] eq ")") {
-			my $lb=pop @lbs;
-			my $rb=$k+1;
-			$table->{$lb}=$rb;
-			$table->{$rb}=$lb;
-		}
-	}
-	if (@lbs) {
-		warn "unbalanced RNA struct.\n";
-	}
-}
-sub which_arm {
-	my $substruct=shift;
-	my $arm;
-	if ($substruct=~/\(/ && $substruct=~/\)/) {
-		$arm="-";
-	}
-	elsif ($substruct=~/\(/) {
-		$arm="5p";
-	}
-	else {
-		$arm="3p";
-	}
-	return $arm;
-}
-sub biggest_bulge {
-	my $struct=shift;
-	my $bulge_size=0;
-	my $max_bulge=0;
-	while ($struct=~/(\.+)/g) {
-		$bulge_size=length $1;
-		if ($bulge_size > $max_bulge) {
-			$max_bulge=$bulge_size;
-		}
-	}
-	return $max_bulge;
-}
-sub get_asy {
-	my($table,$a1,$a2)=@_;
-	my ($pre_i,$pre_j);
-	my $asymmetry=0;
-	foreach my $i ($a1..$a2) {
-		if (defined $table->{$i}) {
-			my $j=$table->{$i};
-			if (defined $pre_i && defined $pre_j) {
-				my $diff=($i-$pre_i)+($j-$pre_j);
-				$asymmetry += abs($diff);
-			}
-			$pre_i=$i;
-			$pre_j=$j;
-		}
-	}
-	return $asymmetry;
-}
-
-sub peaks{
-	my @cluster=@{$_[0]};
-
-	return if(@cluster<1);
-
-	my $max=0; my $index=-1;
-	for (my $i=0;$i<@cluster;$i++) {
-		if($cluster[$i][2]>$max){
-			$max=$cluster[$i][2];
-			$index=$i;
-		}
-	}
-#	&excise(\@cluster,$index,$_[1],$_[2]);
-	return($index);
-}
-
-sub find_cites{
-	my @tmp=@{$_[0]};
-	my $i=&peaks(\@tmp);
-	
-	my $start=$tmp[$i][0];
-	my $total=0; my $node5=0;
-	for (my $j=0;$j<@tmp ;$j++) {
-		$total+=$tmp[$j][2];
-		$node5 +=$tmp[$j][2] if($tmp[$j][0]-$start<=2 && $tmp[$j][0]-$start>=-2);
-	}
-	push @{$cites{$_[1]}{$_[2]}},$tmp[$i] if($node5/$total>0.80 && $tmp[$i][2]/$node5>0.5);
-}
-
-sub newpos{
-	my ($a,$b,$c,$d)=@_;
-	my $s= $a>$c ? $c : $a;
-	my $e=$b>$d ? $b : $d;
-	return($s,$e);
-}
-
-sub rev{
-
-    my($sequence)=@_;
-
-    my $rev=reverse $sequence;   
-
-    return $rev;
-}
-
-sub com{
-
-    my($sequence)=@_;
-
-    $sequence=~tr/acgtuACGTU/TGCAATGCAA/;   
- 
-    return $sequence;
-}
-
-sub revcom{
-
-    my($sequence)=@_;
-
-    my $revcom=rev(com($sequence));
-
-    return $revcom;
-}
-
-sub find_strand{
-
-    #A subroutine to find the strand, parsing different blast formats
-    my($other)=@_;
-
-    my $strand="+";
-
-    if($other=~/-/){
-	$strand="-";
-    }
-
-    if($other=~/minus/i){
-	$strand="-";
-    }
-
-    return($strand);
-}
-sub usage{
-print <<"USAGE";
-Version $version
-Usage:
-$0 -map -g -d -f -o -s -e
-options:
-  -map input file# align result # bst. format
-  -g input file # genome sequence fasta format
-  -d <int>   Maximal space between miRNA and miRNA* (200)
-  -f <int>   Flank sequence length of miRNA precursor (10)
-  -o output file# percursor fasta file
-  -s output file# precursor structure file
-  -e <folat> Maximal free energy allowed for a miRNA precursor (-18 kcal/mol)
-
-  -h help
-USAGE
-exit(1);
-}
-
diff -r 45de5e1ff487 -r 5691802f074b quantify.pl
--- a/quantify.pl	Fri Jul 25 05:57:27 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,495 +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 File::Path;
-use strict;
-use File::Basename;
-#use Getopt::Std;
-use Getopt::Long;
-use RNA;
-
-my %opts;
-GetOptions(\%opts,"r=s","p=s","m=s","mis:i","t:i","e:i","f:i","tag:s","o=s","time:s","h");
-if (!(defined $opts{r} and defined $opts{p} and defined $opts{m} and defined $opts{o} ) || defined $opts{h}) { #necessary arguments
-&usage;
-}
-
-my $read=$opts{'r'};
-my $pre=$opts{'p'};
-my $mature=$opts{'m'};
-
-my $dir=$opts{'o'};
-unless ($dir=~/\/$/) {$dir .="/";}
-if (not -d $dir) {
-	mkdir $dir;
-}
-
-my $threads=defined $opts{'t'} ? $opts{'t'} : 1;
-my $mismatch=defined $opts{'mis'} ?  $opts{'mis'} : 0;
-
-my $upstream = 2;
-my $downstream = 5;
-
-$upstream = $opts{'e'} if(defined $opts{'e'});
-$downstream = $opts{'f'} if(defined $opts{'f'});
-
-my $marks=defined $opts{'tag'} ? $opts{'tag'} : "";
-
-my $time=Time();
-if (defined $opts{'time'}) { $time=$opts{'time'};}
-
-my $tmpdir="${dir}/miRNA_Express_${time}";
-if(not -d $tmpdir){
-	mkdir($tmpdir);
-}
-chdir $tmpdir;
-
-`cp $pre ./`;
-my $pre_file_name=basename($pre);
-
-&mapping(); # matures align to precursors && reads align to precursors;
-
-my %pre_mature; # $pre_mature{pre_id}{matre_ID}{"mature"}[0]->start; $pre_mature{pre_id}{matre_ID}{"mature"}[1]->end;
-&maturePosOnPre(); # acknowledge mature positions on precursor 
-
-my %pre_read;
-&readPosOnPre(); # acknowledge reads positions on precursors
-
-if(!(defined $opts{'tag'})){
-	foreach my $key (keys %pre_read) {
-		$pre_read{$key}[0][0]=~/:([\d|_]+)_x(\d+)$/;
-		my @ss=split/_/,$1;
-		for (my $i=1;$i<=@ss;$i++) {
-			$marks .="Smp$i;";
-		}
-		last;
-	}
-}
-
-my %pre;## read in precursor sequences #$pre{pre_id}="CGTA...."
-&attachPre();
-
-my $preno=scalar (keys %pre);
-print "Total Precursor Number is $preno !!!!\n";
-
-my %struc; #mature  star  loop; $struc{$key}{"struc"}=$str; $struc{$key}{"mfe"}=$mfe;
-&structure();
-
-
-##### analysis and print out  && moRs
-my $aln=$dir."known_microRNA_express.aln";
-my $list=$dir."known_microRNA_express.txt";
-my $moRs=$dir."known_microRNA_express.moRs";
-
-system("ln $mature $dir/known_microRNA_mature.fa ");
-system("ln $pre $dir/known_microRNA_precursor.fa ");
-
-open ALN,">$aln";
-open LIST,">$list";
-open MORS,">$moRs";
-
-$"="\t"; ##### @array print in \t
-
-my @marks=split/\;/,$marks;
-#print LIST "#matueID\tpreID\tpos1\tpos2\tmatureExp\tstarExp\ttotalExp\n";
-print LIST "#matueID\tpreID\tpos1\tpos2";
-for (my $i=0;$i<@marks;$i++) {
-	print LIST "\t",$marks[$i],"_matureExp";
-}
-for (my $i=0;$i<@marks;$i++) {
-	print LIST "\t",$marks[$i],"_starExp";
-}
-for (my $i=0;$i<@marks;$i++) {
-	print LIST "\t",$marks[$i],"_totalExp";
-}
-print LIST "\n";
-print ALN "#>precursor ID \n#precursor sequence\n#precursor structure (mfe)\n#RNA_seq\t@marks\ttotal\n";
-print MORS "#>precursor ID\tstrand\texpress_reads\texpress_reads\/total_reads\tblock_number\tprecursor_sequence\n#\tblock_start\tblock_end\t@marks\ttotal\ttag_number\tsequence\n";
-my %moRs;
-
-foreach my $key (keys %pre) {
-	print ALN ">$key\n$pre{$key}\n$struc{$key}{struc}  ($struc{$key}{mfe})\n";
-	next if(! (exists $pre_read{$key}));
-	my @array=@{$pre_read{$key}};
-	@array=sort{$a->[3]<=> $b->[3]} @array;
-	
-	my $length=length($pre{$key});
-
-	my $maxline=-1;my $max=0; ### storage the maxinum express read line
-	my $totalReadsNo=0; 
-	my @not_over=(); ### new read format better for moRs analysis
-
-####print out Aln file start
-	for (my $i=0;$i<@array;$i++) {
-		my $maps=$array[$i][3]+1;
-		my $mape=$array[$i][3]+length($array[$i][4]);
-		my $str="";
-		$str .= "." x ($maps-1);
-		$str .=$array[$i][4];
-		$str .="." x ($length-$mape);
-		$str .="        ";
-
-		$array[$i][0]=~/:([\d|_]+)_x(\d+)$/;
-		my @sample=split /\_/,$1;
-		my $total=$2;
-		print ALN $str,"@sample","\t",$total,"\n";
-
-		if($total>$max){$max=$total; $maxline=$i;}
-		$totalReadsNo+=$total;
-		
-		push @not_over,[$key,$maps,$mape,$array[$i][0],$total,"+"];
-	}
-####print out Aln file end
-
-#### express list start
-	my ($ms,$me,$ss,$se);
-	if (!(exists($pre_mature{$key}))) {
-		$ms=$array[$maxline][3]+1;
-		$me=$array[$maxline][3]+length($array[$maxline][4]);
-		($ss,$se)=&other_pair($ms,$me,$struc{$key}{'struc'});
-	
-		my ($mexp,$sexp,$texp)=&express($ms-$upstream,$me+$downstream,$ss-$upstream,$se+$downstream,\@array);
-		print LIST "$key\t$key\tmature:$ms..$me\tstar:$ss..$se\t@$mexp\t@$sexp\t@$texp\n";
-	}
-	else{
-		foreach my $maID (keys %{$pre_mature{$key}}) {
-			$ms=$pre_mature{$key}{$maID}{"mature"}[0];
-			$me=$pre_mature{$key}{$maID}{"mature"}[1];
-			$ss=$pre_mature{$key}{$maID}{"star"}[0];
-			$se=$pre_mature{$key}{$maID}{"star"}[1];
-			my ($mexp,$sexp,$texp)=&express($ms-$upstream,$me+$downstream,$ss-$upstream,$se+$downstream,\@array);
-			print LIST "$maID\t$key\tmature:$ms..$me\tstar:$ss..$se\t@$mexp\t@$sexp\t@$texp\n";
-		}
-	}
-#### express list end
-
-#### analysis moRs start
-	my @result; my @m_texp;my $m_texp=0; ### moRs informations
-
-	while (@not_over>0) {
-		my @over=@not_over;
-		@not_over=();
-
-#丰度最高tag
-		my $m_max=0;my $m_maxline=-1;my $m_start=0;my $m_end=0;my $m_exp=0;my @m_exp;my $m_no=1;
-		for (my $i=0;$i<@over;$i++) {
-			my @m_array=@{$over[$i]};
-			if ($m_max<$m_array[4]) {
-				$m_max=$m_array[4];
-				$m_maxline=$i;
-			}
-		}
-		$m_start=$over[$m_maxline][1];
-		$m_end=$over[$m_maxline][2];
-		$m_exp=$m_max;
-		$over[$m_maxline][3]=~/:([\d|_]+)_x(\d+)$/;
-		my @m_nums=split/_/,$1;
-		for (my $j=0;$j<@m_nums;$j++) {
-			$m_exp[$j]=$m_nums[$j];
-		}
-
-#统计以丰度最高tag为坐标的reads, 两端位置差异不超过3nt
-		for (my $i=0;$i<@over;$i++) {
-			next if($i==$m_maxline);
-			my @m_array=@{$over[$i]};
-			if (abs($m_array[1]-$m_start)<=3 && abs($m_array[2]-$m_end)<=3) {
-				$m_exp+=$m_array[4];
-				$m_no++;
-				$m_array[3]=~/:([\d|_]+)_x(\d+)$/;
-				my @m_nums=split/_/,$1;
-				for (my $j=0;$j<@m_nums;$j++) {
-					$m_exp[$j] +=$m_nums[$j];
-				}
-			}
-			elsif($m_array[1]>=$m_end || $m_array[2]<=$m_start){push @not_over,[@{$over[$i]}];} #去除跨越block的reads
-		}
-		if($m_exp>5){### 5个reads
-			$m_texp+=$m_exp;
-			for (my $j=0;$j<@m_exp;$j++) {
-				$m_texp[$j]+=$m_exp[$j];
-			}
-			my $string=&subseq($pre{$key},$m_start,$m_end,"+");
-			push @result,"\t$m_start\t$m_end\t@m_exp\t$m_exp\t$m_no\t$string" ;
-		}
-	}
-
-	my $str=scalar @result;
-	my $percent=sprintf("%.2f",$m_texp/$totalReadsNo);
-	$str=">$key\t+\t$m_texp\t$percent\t".$str."\t$pre{$key}";
-	@{$moRs{$str}}=@result;
-
-#### analysis moRs end
-}
-
-##### moRs print out start
-foreach my $key (keys %moRs) {
-	my @tmp=split/\t/,$key;
-	next if ($tmp[4]<=2);
-	next if($tmp[3]<0.95);
-	my @over;
-	for (my $i=0;$i<@{$moRs{$key}};$i++) {
-		my @arrayi=split/\t/,$moRs{$key}[$i];
-		for (my $j=0;$j<@{$moRs{$key}};$j++) {
-			next if($i==$j);
-			my @arrayj=split/\t/,$moRs{$key}[$j];
-			if ((($arrayj[1]-$arrayi[2]>=0 && $arrayj[1]-$arrayi[2] <=3) || ($arrayj[1]-$arrayi[2]>=18 && $arrayj[1]-$arrayi[2] <=25) )||(($arrayi[1]-$arrayj[2]>=0 && $arrayi[1]-$arrayj[2] <=3)||($arrayi[1]-$arrayj[2]>=18 && $arrayi[1]-$arrayj[2] <=25))) {
-				push @over,$moRs{$key}[$i];
-			}
-		}
-	}
-	if (@over>0) {
-		print MORS "$key\n";
-		foreach  (@{$moRs{$key}}) {
-			print MORS "$_\n";
-		}
-	}
-}
-###### moRs print out end
-close ALN;
-close LIST;
-close MORS;
-
-$"=" ";##### reset
-
-
-################### Sub programs #################
-sub express{
-	my ($ms,$me,$ss,$se,$read)=@_;
-	my (@mexp,@sexp,@texp);
-	$$read[0][0]=~/:([_|\d]+)_x(\d+)$/;
-	my @numsample=split/_/,$1;
-	for (my $i=0;$i<@numsample;$i++) {
-		$mexp[$i]=0;
-		$sexp[$i]=0;
-		$texp[$i]=0;
-	}
-
-	for (my $i=0;$i<@{$read};$i++) {
-		my $start=$$read[$i][3]+1;
-		my $end=$$read[$i][3]+length($$read[$i][4]);
-		$$read[$i][0]=~/:([_|\d]+)_x(\d+)$/;
-		my $expresses=$1;
-		my @nums=split/_/,$expresses;
-		
-		for (my $j=0;$j<@nums;$j++) {
-			$texp[$j]+=$nums[$j];
-		}
-		if ($start>=$ms && $end<=$me) {
-			for (my $j=0;$j<@nums;$j++) {
-				$mexp[$j]+=$nums[$j];
-			}
-		}
-		if ($start>=$ss && $end<=$se) {
-			for (my $j=0;$j<@nums;$j++) {
-				$sexp[$j]+=$nums[$j];
-			}
-		}
-	}
-	return(\@mexp,\@sexp,\@texp);
-}
-
-sub structure{
-	foreach my $key (keys %pre_mature) {
-		if (!(defined $pre{$key})){die "!!!!! No precursor sequence $key, please check it!\n";}
-		my ($str,$mfe)=RNA::fold($pre{$key});
-		$struc{$key}{"struc"}=$str;
-		$struc{$key}{"mfe"}=sprintf ("%.2f",$mfe);
-
-		foreach my $id (keys %{$pre_mature{$key}}) {
-			($pre_mature{$key}{$id}{"star"}[0],$pre_mature{$key}{$id}{"star"}[1])=&other_pair($pre_mature{$key}{$id}{"mature"}[0],$pre_mature{$key}{$id}{"mature"}[1],$str);
-		}
-=cut
-##### Nucleotide complementary 
-		my @tmp=split//,$str;
-		my %a2b;
-		my @bps;
-		for (my $i=0;$i<@tmp;$i++) {
-			if ($tmp[$i] eq "("){push @bps,$i+1 ; next;}
-			if ($tmp[$i] eq ")") {
-				my $up=pop @bps;
-				$a2b{$i+1}=$up;
-				$a2b{$up}=$i+1;
-			}
-		}
-
-##### search star position
-		foreach my $id (keys %{$pre_mature{$key}}) {
-			my $n=0;
-			for (my $i=$pre_mature{$key}{$id}{"mature"}[0];$i<=$pre_mature{$key}{$id}{"mature"}[1] ; $i++) {				
-				if (defined $a2b{$i}) {
-					my $a=$i; my $b=$a2b{$i};
-					if($a>$b){
-						$pre_mature{$key}{$id}{"star"}[0]=$b-$n+2;
-						$pre_mature{$key}{$id}{"star"}[1]=$b-$n+2+($pre_mature{$key}{$id}{"mature"}[1]-$pre_mature{$key}{$id}{"mature"}[0]);
-					}
-					if($a<$b{
-						$pre_mature{$key}{$id}{"star"}[1]=$b+$n+2;
-						$pre_mature{$key}{$id}{"star"}[0]=$b+$n+2-($pre_mature{$key}{$id}{"mature"}[1]-$pre_mature{$key}{$id}{"mature"}[0]);
-					}
-					last;
-				}
-				$n++;
-			}
-		}
-=cut
-	}
-}
-sub other_pair{
-	my ($start,$end,$structure)=@_;
-	##### Nucleotide complementary 
-	my @tmp=split//,$structure;
-	my %a2b;	my @bps;
-	for (my $i=0;$i<@tmp;$i++) {
-		if ($tmp[$i] eq "("){push @bps,$i+1 ; next;}
-		if ($tmp[$i] eq ")") {
-			my $up=pop @bps;
-			$a2b{$i+1}=$up;
-			$a2b{$up}=$i+1;
-		}
-	}
-##### search star position
-	my $n=0;my $startpos; my $endpos;
-	for (my $i=$start;$i<=$end ; $i++) {				
-		if (defined $a2b{$i}) {
-			my $a=$i; my $b=$a2b{$i};
-#			if($a>$b){
-#				$startpos=$b-$n+2;
-#				$endpos=$b-$n+2+($end-$start);
-#			}
-#			if($a<$b){
-				$endpos=$b+$n+2;
-				if($endpos>length($structure)){$endpos=length($structure);}
-				$startpos=$b+$n+2-($end-$start);
-				if($startpos<1){$startpos=1;}
-#			}
-			last;
-		}
-		$n++;
-	}
-	return ($startpos,$endpos);
-}
-sub attachPre{
-	open IN, "<$pre_file_name";
-	my $name;
-	while (my $aline=<IN>) {
-		chomp $aline;
-		if ($aline=~/^>(\S+)/) {
-			$name=$1;
-			next;
-		}
-		$pre{$name} .=$aline;
-	}
-	close IN;
-}
-sub readPosOnPre{
-	open IN,"<read_mapped.bwt";
-	while (my $aline=<IN>) {
-		chomp $aline;
-		my @tmp=split/\t/,$aline;
-		my $id=lc($tmp[2]);
-		push @{$pre_read{$tmp[2]}},[@tmp];
-	}
-	close IN;
-}
-sub maturePosOnPre{
-	open IN,"<mature_mapped.bwt";
-	while (my $aline=<IN>) {
-		chomp $aline;
-		my @tmp=split/\t/,$aline;
-		my $mm=$tmp[0];
-#		$mm=~s/\-3P|\-5P//i;
-		$mm=lc($mm);
-		my $pm=$tmp[2];
-		$pm=lc($pm);
-
-#		next if ($mm ne $pm);### stringent mapping let7a only allowed to map pre-let7a
-		next if($mm!~/$pm/);
-#		print "$tmp[2]\t$tmp[0]\n";
-#		$pre_mature{$tmp[2]}{$tmp[0]}{"mature"}[0]=$tmp[3]-$upstream;
-#		$pre_mature{$tmp[2]}{$tmp[0]}{"mature"}[0]=0 if($pre_mature{$tmp[2]}{$tmp[0]}{"mature"}[0]<0);
-#		$pre_mature{$tmp[2]}{$tmp[0]}{"mature"}[1]=$tmp[3]+length($tmp[4])-1+$downstream;
-		$pre_mature{$tmp[2]}{$tmp[0]}{"mature"}[0]=$tmp[3]+1;
-		$pre_mature{$tmp[2]}{$tmp[0]}{"mature"}[1]=$tmp[3]+length($tmp[4]);
-	}
-	close IN;
-}
-sub mapping{
-    my $err;
-## build bowtie index
-    print STDERR "building bowtie index\n";
-    $err = `bowtie-build $pre_file_name miRNA_precursor`;
-
-## map mature sequences against precursors
-    print STDERR "mapping mature sequences against index\n";
-	$err = `bowtie -p $threads -f -v 0 -a --best --strata --norc miRNA_precursor $mature mature_mapped.bwt`;
-
-## map reads against precursors
-    print STDERR "mapping read sequences against index\n";
-    $err=`bowtie -p $threads -f -v $mismatch -a --best --strata --norc miRNA_precursor $read --al mirbase_mapped.fa --un mirbase_not_mapped.fa read_mapped.bwt `;
-
-}
-
-sub subseq{
-	my $seq=shift;
-	my $beg=shift;
-	my $end=shift;
-	my $strand=shift;
-	
-	my $subseq=substr($seq,$beg-1,$end-$beg+1);
-	if ($strand eq "-") {
-		$subseq=revcom($subseq);
-	}
-	return uc $subseq;
-}
-
-sub revcom{
-	my $seq=shift;
-	$seq=~tr/ATCGatcg/TAGCtagc/;
-	$seq=reverse $seq;
-	return uc $seq;
-}
-
-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 -r -p -m -mis -t -e -f -tag -o -time
-mandatory parameters:
--p precursor.fa  miRNA precursor sequences from miRBase # must be absolute path
--m mature.fa     miRNA sequences from miRBase # must be absolute path
--r reads.fa      your read sequences #must be absolute path
-
--o output directory
-
-options:
--mis [int]     number of allowed mismatches when mapping reads to precursors, default 0
--t [int]     threads number,default 1
--e [int]     number of nucleotides upstream of the mature sequence to consider, default 2
--f [int]     number of nucleotides downstream of the mature sequence to consider, default 5
--tag [string] sample marks# eg. sampleA;sampleB;sampleC
--time sting #make directory time,default is the local time
--h help
-USAGE
-exit(1);
-}
-
diff -r 45de5e1ff487 -r 5691802f074b rfam.pl
--- a/rfam.pl	Fri Jul 25 05:57:27 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,103 +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;
-use File::Basename;
-
-my %opts;
-GetOptions(\%opts,"i=s","ref=s","index:s","v:i","p:i","o=s","time:s","h");
-if (!(defined $opts{i} and defined $opts{o} ) || defined $opts{h}) { #necessary arguments
-&usage;
-}
-
-my $filein=$opts{'i'};
-my $dir=$opts{'o'};
-unless ($dir=~/\/$/) {$dir.="/";}
-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;
-
-if (not -d $dir) {
-	mkdir $dir;
-}
-
-
-my $time=Time();
-if (defined $opts{'time'}) {
-	$time=$opts{'time'};
-}
-my $mapdir=$dir."/rfam_match_".$time;
-if(not -d $mapdir){
-	mkdir $mapdir;
-}
-chdir $mapdir;
-###check genome index
-if (-s $index.".1.ebwt") {
-}else{
-	&checkACGT($rfam);
-	`bowtie-build $rfam`;
-	$index="$rfam";
-}
-### 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 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:
-$0 -i -o
-options:
--i input file# input reads fasta/fastq file
--ref input file# rfam file, which do not contain miRNAs
--index file-prefix #(must be indexed by bowtie-build) The parameter
-                string must be the prefix of the bowtie index. For instance, if
-                the first indexed file is called 'h_sapiens_37_asm.1.ebwt' then
-                the prefix is 'h_sapiens_37_asm'.##can be null
--v <int>           report end-to-end hits w/ <=v mismatches; ignore qualities,default 0;
-
--p/--threads <int> number of alignment threads to launch (default: 1)
-
--o output directory 
--time sting #make directory time,default is the local time
--h help
-USAGE
-exit(1);
-}
-
diff -r 45de5e1ff487 -r 5691802f074b tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Jul 25 05:57:27 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,28 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="fastx_toolkit" version="0.0.13">
-        <repository changeset_revision="ec66ae4c269b" name="package_fastx_toolkit_0_0_13" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="bowtie" version="0.12.7">
-        <repository changeset_revision="9f9f38617a98" name="package_bowtie_0_12_7" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
-    </package>
-    <set_environment version="1.0">
-        <environment_variable action="set_to" name="SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
-    </set_environment>
-    <package name="R" version="2.11.0">
-        <repository changeset_revision="8d0a55bf7aaf" name="package_r_2_11_0" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
-    </package>
-	<package name="ViennaRNA" version="1.5">
-	   <install version="1.0">
-		   <actions>
-		     <action type="download_by_url">http://web.mit.edu/seven/src/ViennaRNA-1.5beta.tar.gz</action>
-			 <action type="shell_command">./configure --prefix=$INSTALL_DIR --datadir=$INSTALL_DIR</action>
-			 <action type="shell_command">make</action>
-			 <action type="shell_command">make install</action>
-			 <action type="set_environment">
-			   <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-			 </action>
-		   </actions>
-	   </install>
-	</package>
-</tool_dependency>