--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/count_rfam_express.pl	Fri Jul 25 05:20:08 2014 -0400
@@ -0,0 +1,1800 @@
+#!/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
+RF00692	miRNA
+RF00693	miRNA
+RF00694	miRNA
+RF00695	miRNA
+RF00696	miRNA
+RF00697	miRNA
+RF00698	miRNA
+RF00699	miRNA
+RF00700	miRNA
+RF00701	miRNA
+RF00702	miRNA
+RF00703	miRNA
+RF00704	miRNA
+RF00705	miRNA
+RF00706	miRNA
+RF00707	miRNA
+RF00708	miRNA
+RF00709	miRNA
+RF00710	miRNA
+RF00711	miRNA
+RF00712	miRNA
+RF00713	miRNA
+RF00714	miRNA
+RF00715	miRNA
+RF00716	miRNA
+RF00717	miRNA
+RF00718	miRNA
+RF00719	miRNA
+RF00720	miRNA
+RF00721	miRNA
+RF00722	miRNA
+RF00723	miRNA
+RF00724	miRNA
+RF00725	miRNA
+RF00726	miRNA
+RF00727	miRNA
+RF00728	miRNA
+RF00729	miRNA
+RF00730	miRNA
+RF00731	miRNA
+RF00732	miRNA
+RF00733	miRNA
+RF00734	miRNA
+RF00735	miRNA
+RF00736	miRNA
+RF00737	miRNA
+RF00739	miRNA
+RF00740	miRNA
+RF00741	miRNA
+RF00742	miRNA
+RF00743	miRNA
+RF00744	miRNA
+RF00745	miRNA
+RF00746	miRNA
+RF00747	miRNA
+RF00748	miRNA
+RF00749	miRNA
+RF00750	miRNA
+RF00751	miRNA
+RF00752	miRNA
+RF00753	miRNA
+RF00754	miRNA
+RF00755	miRNA
+RF00756	miRNA
+RF00757	miRNA
+RF00758	miRNA
+RF00760	miRNA
+RF00761	miRNA
+RF00762	miRNA
+RF00763	miRNA
+RF00764	miRNA
+RF00765	miRNA
+RF00766	miRNA
+RF00767	miRNA
+RF00768	miRNA
+RF00769	miRNA
+RF00770	miRNA
+RF00771	miRNA
+RF00772	miRNA
+RF00773	miRNA
+RF00774	miRNA
+RF00775	miRNA
+RF00776	miRNA
+RF00777	miRNA
+RF00778	miRNA
+RF00779	miRNA
+RF00780	miRNA
+RF00781	miRNA
+RF00782	miRNA
+RF00783	miRNA
+RF00784	miRNA
+RF00785	miRNA
+RF00786	miRNA
+RF00787	miRNA
+RF00788	miRNA
+RF00789	miRNA
+RF00790	miRNA
+RF00791	miRNA
+RF00792	miRNA
+RF00793	miRNA
+RF00794	miRNA
+RF00795	miRNA
+RF00796	miRNA
+RF00797	miRNA
+RF00798	miRNA
+RF00799	miRNA
+RF00800	miRNA
+RF00801	miRNA
+RF00802	miRNA
+RF00803	miRNA
+RF00804	miRNA
+RF00805	miRNA
+RF00806	miRNA
+RF00807	miRNA
+RF00808	miRNA
+RF00809	miRNA
+RF00810	miRNA
+RF00811	miRNA
+RF00812	miRNA
+RF00813	miRNA
+RF00814	miRNA
+RF00815	miRNA
+RF00816	miRNA
+RF00817	miRNA
+RF00818	miRNA
+RF00819	miRNA
+RF00820	miRNA
+RF00821	miRNA
+RF00822	miRNA
+RF00823	miRNA
+RF00824	miRNA
+RF00825	miRNA
+RF00826	miRNA
+RF00827	miRNA
+RF00828	miRNA
+RF00829	miRNA
+RF00830	miRNA
+RF00831	miRNA
+RF00832	miRNA
+RF00833	miRNA
+RF00834	miRNA
+RF00835	miRNA
+RF00836	miRNA
+RF00837	miRNA
+RF00838	miRNA
+RF00839	miRNA
+RF00840	miRNA
+RF00841	miRNA
+RF00842	miRNA
+RF00843	miRNA
+RF00844	miRNA
+RF00845	miRNA
+RF00846	miRNA
+RF00847	miRNA
+RF00848	miRNA
+RF00849	miRNA
+RF00850	miRNA
+RF00851	miRNA
+RF00852	miRNA
+RF00853	miRNA
+RF00854	miRNA
+RF00855	miRNA
+RF00856	miRNA
+RF00857	miRNA
+RF00858	miRNA
+RF00859	miRNA
+RF00861	miRNA
+RF00862	miRNA
+RF00863	miRNA
+RF00864	miRNA
+RF00865	miRNA
+RF00866	miRNA
+RF00867	miRNA
+RF00868	miRNA
+RF00869	miRNA
+RF00870	miRNA
+RF00871	miRNA
+RF00872	miRNA
+RF00873	miRNA
+RF00874	miRNA
+RF00875	miRNA
+RF00876	miRNA
+RF00877	miRNA
+RF00878	miRNA
+RF00879	miRNA
+RF00882	miRNA
+RF00883	miRNA
+RF00884	miRNA
+RF00885	miRNA
+RF00886	miRNA
+RF00887	miRNA
+RF00888	miRNA
+RF00890	miRNA
+RF00891	miRNA
+RF00892	miRNA
+RF00893	miRNA
+RF00894	miRNA
+RF00895	miRNA
+RF00896	miRNA
+RF00897	miRNA
+RF00898	miRNA
+RF00899	miRNA
+RF00900	miRNA
+RF00901	miRNA
+RF00902	miRNA
+RF00903	miRNA
+RF00904	miRNA
+RF00905	miRNA
+RF00906	miRNA
+RF00907	miRNA
+RF00908	miRNA
+RF00909	miRNA
+RF00910	miRNA
+RF00911	miRNA
+RF00912	miRNA
+RF00914	miRNA
+RF00915	miRNA
+RF00917	miRNA
+RF00918	miRNA
+RF00919	miRNA
+RF00920	miRNA
+RF00921	miRNA
+RF00922	miRNA
+RF00925	miRNA
+RF00926	miRNA
+RF00927	miRNA
+RF00928	miRNA
+RF00929	miRNA
+RF00931	miRNA
+RF00932	miRNA
+RF00933	miRNA
+RF00934	miRNA
+RF00935	miRNA
+RF00936	miRNA
+RF00937	miRNA
+RF00939	miRNA
+RF00940	miRNA
+RF00941	miRNA
+RF00942	miRNA
+RF00943	miRNA
+RF00945	miRNA
+RF00946	miRNA
+RF00947	miRNA
+RF00948	miRNA
+RF00949	miRNA
+RF00950	miRNA
+RF00951	miRNA
+RF00952	miRNA
+RF00953	miRNA
+RF00954	miRNA
+RF00955	miRNA
+RF00956	miRNA
+RF00957	miRNA
+RF00958	miRNA
+RF00959	miRNA
+RF00960	miRNA
+RF00961	miRNA
+RF00962	miRNA
+RF00963	miRNA
+RF00964	miRNA
+RF00965	miRNA
+RF00966	miRNA
+RF00967	miRNA
+RF00968	miRNA
+RF00969	miRNA
+RF00970	miRNA
+RF00971	miRNA
+RF00972	miRNA
+RF00973	miRNA
+RF00974	miRNA
+RF00975	miRNA
+RF00976	miRNA
+RF00977	miRNA
+RF00978	miRNA
+RF00979	miRNA
+RF00980	miRNA
+RF00981	miRNA
+RF00983	miRNA
+RF00984	miRNA
+RF00985	miRNA
+RF00986	miRNA
+RF00987	miRNA
+RF00988	miRNA
+RF00989	miRNA
+RF00990	miRNA
+RF00991	miRNA
+RF00992	miRNA
+RF00993	miRNA
+RF00994	miRNA
+RF00995	miRNA
+RF00996	miRNA
+RF00997	miRNA
+RF00998	miRNA
+RF00999	miRNA
+RF01000	miRNA
+RF01001	miRNA
+RF01002	miRNA
+RF01003	miRNA
+RF01004	miRNA
+RF01005	miRNA
+RF01006	miRNA
+RF01007	miRNA
+RF01008	miRNA
+RF01009	miRNA
+RF01010	miRNA
+RF01011	miRNA
+RF01012	miRNA
+RF01013	miRNA
+RF01014	miRNA
+RF01015	miRNA
+RF01016	miRNA
+RF01017	miRNA
+RF01018	miRNA
+RF01019	miRNA
+RF01020	miRNA
+RF01021	miRNA
+RF01022	miRNA
+RF01023	miRNA
+RF01024	miRNA
+RF01025	miRNA
+RF01026	miRNA
+RF01027	miRNA
+RF01028	miRNA
+RF01029	miRNA
+RF01030	miRNA
+RF01031	miRNA
+RF01032	miRNA
+RF01033	miRNA
+RF01034	miRNA
+RF01035	miRNA
+RF01036	miRNA
+RF01037	miRNA
+RF01038	miRNA
+RF01039	miRNA
+RF01040	miRNA
+RF01041	miRNA
+RF01042	miRNA
+RF01043	miRNA
+RF01044	miRNA
+RF01045	miRNA
+RF01059	miRNA
+RF01061	miRNA
+RF01063	miRNA
+RF01064	miRNA
+RF01117	miRNA
+RF01314	miRNA
+RF01413	miRNA
+RF01895	miRNA
+RF01896	miRNA
+RF01897	miRNA
+RF01898	miRNA
+RF01899	miRNA
+RF01900	miRNA
+RF01901	miRNA
+RF01902	miRNA
+RF01903	miRNA
+RF01910	miRNA
+RF01911	miRNA
+RF01912	miRNA
+RF01913	miRNA
+RF01914	miRNA
+RF01915	miRNA
+RF01916	miRNA
+RF01917	miRNA
+RF01918	miRNA
+RF01919	miRNA
+RF01920	miRNA
+RF01921	miRNA
+RF01922	miRNA
+RF01923	miRNA
+RF01924	miRNA
+RF01925	miRNA
+RF01926	miRNA
+RF01927	miRNA
+RF01936	miRNA
+RF01937	miRNA
+RF01938	miRNA
+RF01939	miRNA
+RF01940	miRNA
+RF01941	miRNA
+RF01942	miRNA
+RF01943	miRNA
+RF01944	miRNA
+RF01945	miRNA
+RF01996	miRNA
+RF01997	miRNA
+RF02000	miRNA
+RF02002	miRNA
+RF02006	miRNA
+RF02007	miRNA
+RF02008	miRNA
+RF02009	miRNA
+RF02010	miRNA
+RF02011	miRNA
+RF02013	miRNA
+RF02014	miRNA
+RF02015	miRNA
+RF02016	miRNA
+RF02017	miRNA
+RF02018	miRNA
+RF02019	miRNA
+RF02020	miRNA
+RF02021	miRNA
+RF02022	miRNA
+RF02023	miRNA
+RF02024	miRNA
+RF02025	miRNA
+RF02026	miRNA
+RF02027	miRNA
+RF02028	miRNA
+RF02061	miRNA
+RF02092	miRNA
+RF02093	miRNA
+RF02094	miRNA
+RF02095	miRNA
+RF02096	miRNA
+RF02097	miRNA
+RF02214	miRNA
+RF02244	miRNA
+RF02245	miRNA
+RF02254	miRNA
+RF00001	rRNA
+RF00002	rRNA
+RF01118	rRNA
+RF01960	rRNA
+RF00177	rRNA
+RF01959	rRNA
+RF00003	snRNA
+RF00004	snRNA
+RF00007	snRNA
+RF00012	snRNA
+RF00015	snRNA
+RF00016	snRNA
+RF00020	snRNA
+RF00026	snRNA
+RF00045	snRNA
+RF00046	snRNA
+RF00049	snRNA
+RF00054	snRNA
+RF00055	snRNA
+RF00056	snRNA
+RF00065	snRNA
+RF00066	snRNA
+RF00067	snRNA
+RF00068	snRNA
+RF00069	snRNA
+RF00070	snRNA
+RF00071	snRNA
+RF00072	snRNA
+RF00085	snRNA
+RF00086	snRNA
+RF00087	snRNA
+RF00088	snRNA
+RF00089	snRNA
+RF00090	snRNA
+RF00091	snRNA
+RF00092	snRNA
+RF00093	snRNA
+RF00095	snRNA
+RF00096	snRNA
+RF00097	snRNA
+RF00099	snRNA
+RF00105	snRNA
+RF00108	snRNA
+RF00132	snRNA
+RF00133	snRNA
+RF00134	snRNA
+RF00135	snRNA
+RF00136	snRNA
+RF00137	snRNA
+RF00138	snRNA
+RF00139	snRNA
+RF00142	snRNA
+RF00145	snRNA
+RF00147	snRNA
+RF00149	snRNA
+RF00150	snRNA
+RF00151	snRNA
+RF00152	snRNA
+RF00153	snRNA
+RF00154	snRNA
+RF00155	snRNA
+RF00156	snRNA
+RF00157	snRNA
+RF00158	snRNA
+RF00159	snRNA
+RF00160	snRNA
+RF00181	snRNA
+RF00186	snRNA
+RF00187	snRNA
+RF00188	snRNA
+RF00189	snRNA
+RF00190	snRNA
+RF00191	snRNA
+RF00200	snRNA
+RF00201	snRNA
+RF00202	snRNA
+RF00203	snRNA
+RF00204	snRNA
+RF00205	snRNA
+RF00206	snRNA
+RF00208	snRNA
+RF00211	snRNA
+RF00212	snRNA
+RF00213	snRNA
+RF00217	snRNA
+RF00218	snRNA
+RF00221	snRNA
+RF00231	snRNA
+RF00263	snRNA
+RF00264	snRNA
+RF00265	snRNA
+RF00266	snRNA
+RF00267	snRNA
+RF00268	snRNA
+RF00270	snRNA
+RF00271	snRNA
+RF00272	snRNA
+RF00273	snRNA
+RF00274	snRNA
+RF00275	snRNA
+RF00276	snRNA
+RF00277	snRNA
+RF00278	snRNA
+RF00279	snRNA
+RF00280	snRNA
+RF00281	snRNA
+RF00282	snRNA
+RF00283	snRNA
+RF00284	snRNA
+RF00285	snRNA
+RF00286	snRNA
+RF00287	snRNA
+RF00288	snRNA
+RF00289	snRNA
+RF00291	snRNA
+RF00292	snRNA
+RF00293	snRNA
+RF00294	snRNA
+RF00295	snRNA
+RF00296	snRNA
+RF00300	snRNA
+RF00301	snRNA
+RF00302	snRNA
+RF00303	snRNA
+RF00304	snRNA
+RF00305	snRNA
+RF00306	snRNA
+RF00307	snRNA
+RF00309	snRNA
+RF00310	snRNA
+RF00311	snRNA
+RF00312	snRNA
+RF00313	snRNA
+RF00314	snRNA
+RF00315	snRNA
+RF00316	snRNA
+RF00317	snRNA
+RF00318	snRNA
+RF00319	snRNA
+RF00320	snRNA
+RF00321	snRNA
+RF00322	snRNA
+RF00323	snRNA
+RF00324	snRNA
+RF00325	snRNA
+RF00326	snRNA
+RF00327	snRNA
+RF00328	snRNA
+RF00329	snRNA
+RF00330	snRNA
+RF00331	snRNA
+RF00332	snRNA
+RF00333	snRNA
+RF00334	snRNA
+RF00335	snRNA
+RF00336	snRNA
+RF00337	snRNA
+RF00338	snRNA
+RF00339	snRNA
+RF00340	snRNA
+RF00341	snRNA
+RF00342	snRNA
+RF00343	snRNA
+RF00344	snRNA
+RF00345	snRNA
+RF00348	snRNA
+RF00349	snRNA
+RF00350	snRNA
+RF00351	snRNA
+RF00352	snRNA
+RF00353	snRNA
+RF00355	snRNA
+RF00356	snRNA
+RF00357	snRNA
+RF00358	snRNA
+RF00359	snRNA
+RF00360	snRNA
+RF00361	snRNA
+RF00377	snRNA
+RF00392	snRNA
+RF00393	snRNA
+RF00394	snRNA
+RF00396	snRNA
+RF00397	snRNA
+RF00398	snRNA
+RF00399	snRNA
+RF00400	snRNA
+RF00401	snRNA
+RF00402	snRNA
+RF00403	snRNA
+RF00404	snRNA
+RF00405	snRNA
+RF00406	snRNA
+RF00407	snRNA
+RF00408	snRNA
+RF00409	snRNA
+RF00410	snRNA
+RF00411	snRNA
+RF00412	snRNA
+RF00413	snRNA
+RF00414	snRNA
+RF00415	snRNA
+RF00416	snRNA
+RF00417	snRNA
+RF00418	snRNA
+RF00419	snRNA
+RF00420	snRNA
+RF00421	snRNA
+RF00422	snRNA
+RF00423	snRNA
+RF00424	snRNA
+RF00425	snRNA
+RF00426	snRNA
+RF00427	snRNA
+RF00428	snRNA
+RF00429	snRNA
+RF00430	snRNA
+RF00431	snRNA
+RF00432	snRNA
+RF00438	snRNA
+RF00439	snRNA
+RF00440	snRNA
+RF00441	snRNA
+RF00443	snRNA
+RF00471	snRNA
+RF00472	snRNA
+RF00473	snRNA
+RF00474	snRNA
+RF00475	snRNA
+RF00476	snRNA
+RF00477	snRNA
+RF00478	snRNA
+RF00479	snRNA
+RF00482	snRNA
+RF00488	snRNA
+RF00492	snRNA
+RF00493	snRNA
+RF00494	snRNA
+RF00509	snRNA
+RF00526	snRNA
+RF00527	snRNA
+RF00528	snRNA
+RF00529	snRNA
+RF00530	snRNA
+RF00531	snRNA
+RF00532	snRNA
+RF00533	snRNA
+RF00535	snRNA
+RF00536	snRNA
+RF00537	snRNA
+RF00538	snRNA
+RF00539	snRNA
+RF00540	snRNA
+RF00541	snRNA
+RF00542	snRNA
+RF00543	snRNA
+RF00544	snRNA
+RF00545	snRNA
+RF00546	snRNA
+RF00548	snRNA
+RF00553	snRNA
+RF00554	snRNA
+RF00560	snRNA
+RF00561	snRNA
+RF00562	snRNA
+RF00563	snRNA
+RF00564	snRNA
+RF00565	snRNA
+RF00566	snRNA
+RF00567	snRNA
+RF00568	snRNA
+RF00569	snRNA
+RF00570	snRNA
+RF00571	snRNA
+RF00572	snRNA
+RF00573	snRNA
+RF00574	snRNA
+RF00575	snRNA
+RF00576	snRNA
+RF00577	snRNA
+RF00578	snRNA
+RF00579	snRNA
+RF00580	snRNA
+RF00581	snRNA
+RF00582	snRNA
+RF00584	snRNA
+RF00586	snRNA
+RF00588	snRNA
+RF00591	snRNA
+RF00592	snRNA
+RF00593	snRNA
+RF00594	snRNA
+RF00598	snRNA
+RF00599	snRNA
+RF00600	snRNA
+RF00601	snRNA
+RF00602	snRNA
+RF00603	snRNA
+RF00604	snRNA
+RF00606	snRNA
+RF00607	snRNA
+RF00608	snRNA
+RF00609	snRNA
+RF00610	snRNA
+RF00611	snRNA
+RF00612	snRNA
+RF00613	snRNA
+RF00614	snRNA
+RF00618	snRNA
+RF00619	snRNA
+RF01119	snRNA
+RF01120	snRNA
+RF01121	snRNA
+RF01122	snRNA
+RF01123	snRNA
+RF01124	snRNA
+RF01125	snRNA
+RF01126	snRNA
+RF01127	snRNA
+RF01128	snRNA
+RF01129	snRNA
+RF01130	snRNA
+RF01131	snRNA
+RF01132	snRNA
+RF01133	snRNA
+RF01134	snRNA
+RF01135	snRNA
+RF01136	snRNA
+RF01137	snRNA
+RF01138	snRNA
+RF01139	snRNA
+RF01140	snRNA
+RF01141	snRNA
+RF01142	snRNA
+RF01143	snRNA
+RF01144	snRNA
+RF01145	snRNA
+RF01146	snRNA
+RF01147	snRNA
+RF01148	snRNA
+RF01149	snRNA
+RF01150	snRNA
+RF01151	snRNA
+RF01152	snRNA
+RF01153	snRNA
+RF01155	snRNA
+RF01156	snRNA
+RF01157	snRNA
+RF01158	snRNA
+RF01159	snRNA
+RF01160	snRNA
+RF01161	snRNA
+RF01162	snRNA
+RF01163	snRNA
+RF01164	snRNA
+RF01165	snRNA
+RF01166	snRNA
+RF01167	snRNA
+RF01168	snRNA
+RF01169	snRNA
+RF01170	snRNA
+RF01171	snRNA
+RF01172	snRNA
+RF01173	snRNA
+RF01174	snRNA
+RF01175	snRNA
+RF01176	snRNA
+RF01177	snRNA
+RF01178	snRNA
+RF01179	snRNA
+RF01180	snRNA
+RF01181	snRNA
+RF01182	snRNA
+RF01183	snRNA
+RF01184	snRNA
+RF01185	snRNA
+RF01186	snRNA
+RF01188	snRNA
+RF01189	snRNA
+RF01190	snRNA
+RF01191	snRNA
+RF01192	snRNA
+RF01193	snRNA
+RF01194	snRNA
+RF01195	snRNA
+RF01196	snRNA
+RF01197	snRNA
+RF01198	snRNA
+RF01199	snRNA
+RF01200	snRNA
+RF01201	snRNA
+RF01202	snRNA
+RF01203	snRNA
+RF01204	snRNA
+RF01205	snRNA
+RF01206	snRNA
+RF01207	snRNA
+RF01208	snRNA
+RF01209	snRNA
+RF01210	snRNA
+RF01211	snRNA
+RF01212	snRNA
+RF01213	snRNA
+RF01214	snRNA
+RF01215	snRNA
+RF01216	snRNA
+RF01218	snRNA
+RF01219	snRNA
+RF01220	snRNA
+RF01221	snRNA
+RF01222	snRNA
+RF01223	snRNA
+RF01224	snRNA
+RF01225	snRNA
+RF01226	snRNA
+RF01227	snRNA
+RF01228	snRNA
+RF01229	snRNA
+RF01230	snRNA
+RF01231	snRNA
+RF01232	snRNA
+RF01233	snRNA
+RF01234	snRNA
+RF01235	snRNA
+RF01236	snRNA
+RF01237	snRNA
+RF01238	snRNA
+RF01239	snRNA
+RF01240	snRNA
+RF01241	snRNA
+RF01242	snRNA
+RF01243	snRNA
+RF01244	snRNA
+RF01245	snRNA
+RF01246	snRNA
+RF01247	snRNA
+RF01248	snRNA
+RF01249	snRNA
+RF01250	snRNA
+RF01251	snRNA
+RF01252	snRNA
+RF01253	snRNA
+RF01254	snRNA
+RF01255	snRNA
+RF01256	snRNA
+RF01257	snRNA
+RF01258	snRNA
+RF01259	snRNA
+RF01260	snRNA
+RF01261	snRNA
+RF01262	snRNA
+RF01263	snRNA
+RF01264	snRNA
+RF01265	snRNA
+RF01266	snRNA
+RF01267	snRNA
+RF01268	snRNA
+RF01269	snRNA
+RF01270	snRNA
+RF01271	snRNA
+RF01272	snRNA
+RF01273	snRNA
+RF01274	snRNA
+RF01275	snRNA
+RF01276	snRNA
+RF01277	snRNA
+RF01278	snRNA
+RF01279	snRNA
+RF01280	snRNA
+RF01281	snRNA
+RF01283	snRNA
+RF01284	snRNA
+RF01285	snRNA
+RF01286	snRNA
+RF01287	snRNA
+RF01288	snRNA
+RF01289	snRNA
+RF01290	snRNA
+RF01291	snRNA
+RF01292	snRNA
+RF01293	snRNA
+RF01294	snRNA
+RF01295	snRNA
+RF01296	snRNA
+RF01297	snRNA
+RF01298	snRNA
+RF01299	snRNA
+RF01300	snRNA
+RF01301	snRNA
+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