# HG changeset patch
# User tyty
# Date 1410807163 14400
# Node ID a292aaf517356ea52541a328f277561ae31db91c
# Parent  f4cc06e925309dc933b42c8c6ce2eb2c3af422c3
Uploaded

diff -r f4cc06e92530 -r a292aaf51735 Iterative_mapping/iterative_map.py
--- a/Iterative_mapping/iterative_map.py	Mon Sep 15 14:52:20 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,103 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-import sys
-import os
-from read_file import *
-from read_s_file import *
-
-type_input = sys.argv[1]
-seq_file = sys.argv[2]
-ref_file = sys.argv[3]
-shift = sys.argv[4]
-length = sys.argv[5]
-map_type = sys.argv[6]
-output_file = sys.argv[7]
-
-
-if map_type!="default":
-    s = ""
-    s = s+"-v "+sys.argv[8]
-    s = s+" -5 "+sys.argv[9]
-    s = s+" -3 "+sys.argv[10]
-    s = s+" -k "+sys.argv[11]
-    if sys.argv[12]:
-        s = s+" -a"
-    if int(sys.argv[13])>=1:
-        s = s+" -m "+sys.argv[13]
-    if sys.argv[14]:
-        s = s+" --best --strata "
-    
-else:
-    s = "-v 3 -a --best --strata "
-
-ospath = os.path.realpath(sys.argv[0])
-ost = ospath.split('/')
-syspath = ""
-for i in range(len(ost)-1):
-    syspath = syspath+ost[i].strip()
-    syspath = syspath+'/'
-
-os.system("bowtie-build -f "+ref_file+" "+syspath+"ref > "+syspath+"log.txt")
-
-os.system("cp "+seq_file+" "+syspath+"seq0.fa")
-
-if type_input == "fasta":
-    tp = 'fasta'
-if type_input == "fastq":
-    tp = 'fastq'
-
-k = 0
-print(type_input)
-while(True):
-    if type_input == "fasta":
-        os.system("bowtie "+s+"-f "+syspath+"ref"+" "+syspath+"seq"+str(k)+".fa --quiet -S > "+syspath+"map"+str(k)+".sam")
-    if type_input == "fastq":
-        os.system("bowtie "+s+"-q "+syspath+"ref"+" "+syspath+"seq"+str(k)+".fa --quiet -S > "+syspath+"map"+str(k)+".sam")
-    os.system("samtools view -Sb -F 0xfff "+syspath+"map"+str(k)+".sam > "+syspath+"mapped"+str(k)+".bam 2>"+syspath+"log.txt") #get mapped reads
-    os.system("samtools view -Sb -f 0x4 "+syspath+"map"+str(k)+".sam > "+syspath+"umapped"+str(k)+".bam 2>"+syspath+"log.txt") #get unmapped reads
-    os.system("samtools view -Sb -f 0x10 "+syspath+"map"+str(k)+".sam > "+syspath+"rmapped"+str(k)+".bam 2>"+syspath+"log.txt") #get reversed mapped reads
-    os.system("samtools merge -f "+syspath+"unmapped"+str(k)+".bam "+syspath+"umapped"+str(k)+".bam "+syspath+"rmapped"+str(k)+".bam") #get reversed mapped reads
-    os.system("samtools view -h -o "+syspath+"unmapped"+str(k)+".sam "+syspath+"unmapped"+str(k)+".bam") #get reversed mapped reads
-    if k>0:
-        os.system("samtools view -h -o "+syspath+"mapped"+str(k)+".sam "+syspath+"mapped"+str(k)+".bam") #get reversed mapped reads
-        os.system("cut -f 1 "+syspath+"unmapped"+str(k)+".sam > "+syspath+"unmapped"+str(k)+".txt")
-        os.system("cut -f 1 "+syspath+"mapped"+str(k)+".sam > "+syspath+"mapped"+str(k)+".txt")
-        os.system("python "+syspath+"remove_map.py "+syspath+"unmapped"+str(k)+".txt "+syspath+"mapped"+str(k)+".txt "+syspath+"runmapped"+str(k)+".txt")
-        os.system("rm "+syspath+"mapped"+str(k)+".sam")
-        os.system("rm "+syspath+"mapped"+str(k)+".txt")
-        os.system("rm "+syspath+"unmapped"+str(k)+".txt")
-    else:
-        os.system("cut -f 1 "+syspath+"unmapped"+str(k)+".sam > "+syspath+"runmapped"+str(k)+".txt")
-    
-    os.system("rm "+syspath+"unmapped"+str(k)+".bam")
-    os.system("rm "+syspath+"umapped"+str(k)+".bam")
-    os.system("rm "+syspath+"rmapped"+str(k)+".bam")
-    os.system("python "+syspath+"seq_track.py "+syspath+"runmapped"+str(k)+".txt "+syspath+"seq"+str(k)+".fa "+syspath+"unmap_seq"+str(k)+".fa "+tp) #get unmapped sequence
-    os.system("python "+syspath+"truncate.py "+syspath+"unmap_seq"+str(k)+".fa "+shift+" "+syspath+"seq"+str(k+1)+".fa "+length) #truncate unmapped sequence
-    os.system("rm "+syspath+"seq"+str(k)+".fa") #Remove sequences being mapped
-    os.system("rm "+syspath+"map"+str(k)+".sam") #Remove mapping file
-    os.system("rm "+syspath+"unmap_seq"+str(k)+".fa") #Remove unmapped sequnce
-    os.system("rm "+syspath+"runmapped"+str(k)+".txt")
-    os.system("rm "+syspath+"unmapped"+str(k)+".sam")
-    
-    os.system("wc -l "+syspath+"seq"+str(k+1)+".fa > "+syspath+"count"+str(k+1)+".txt")
-    c = read_sp_file(syspath+"count"+str(k+1)+".txt")
-    if c[0][0] == '0': #If no reads is in the sequence file, stop
-        os.system("rm "+syspath+"count"+str(k+1)+".txt")
-        os.system("rm "+syspath+"seq"+str(k+1)+".fa")
-        break
-    os.system("rm "+syspath+"count"+str(k+1)+".txt")
-    k = k+1
-
-ss = ""
-for i in range(0,k+1):
-    ss = ss+" "+syspath+"mapped"+str(i)+".bam"
-
-
-os.system("samtools merge -f "+output_file+" "+ss)
-#print("samtools merge mapped_all.bam"+ss)
-os.system("rm "+syspath+"mapped*.bam")
-os.system("rm "+syspath+"ref*")
-
-
diff -r f4cc06e92530 -r a292aaf51735 Iterative_mapping/iterative_map.xml
--- a/Iterative_mapping/iterative_map.xml	Mon Sep 15 14:52:20 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,80 +0,0 @@
-<tool id="iterative_map_pipeline" name="Iterative mapping" version="1.0">
-	<description></description>
-	<command interpreter="python">
-        #if $mapping_file.type == "user"
-            iterative_map.py $file_format.type $file_format.seq_file $reference_file $shift $length $mapping_file.type $output $mapping_file.param_v $mapping_file.param_five $mapping_file.param_three $mapping_file.param_k $mapping_file.param_a $mapping_file.param_m $mapping_file.param_best  
-        #else
-            iterative_map.py $file_format.type $file_format.seq_file $reference_file $shift $length $mapping_file.type $output
-        #end if
-    </command>
-        <requirements>
-                <requirement type="package" version="1.61">biopython</requirement>
-                <requirement type="package" version="1.7">numpy</requirement>
-                <requirement type="package" version="0.1.18">samtools</requirement>
-                <requirement type="package" version="0.12.7">bowtie</requirement>
-        </requirements>
-	<inputs>
-                <conditional name="file_format">
-                  <param name="type" type="select" label="Format of the file of the reads (Default FASTQ)">
-                    <option value="fastq">FASTQ</option>
-                    <option value="fasta">FASTA</option>
-                  </param>
-                  <when value="fastq">
-                    <param name="seq_file" type="data" format="fastq" label="Fastq file"/>
-                  </when>
-                  <when value="fasta">
-                    <param name="seq_file" type="data" format="fasta" label="Fasta file"/>
-                  </when>
-                </conditional>
-		<param name="reference_file" type="data" format="fasta" label="Reference genome/transcriptome"/>
-                <param name="shift" type="integer" value="1" label="Number of nucleotide trimmed each round"/>
-                <param name="length" type="integer" value="21" label="Minimum requirement of read length for mapping"/>
-                <conditional name="mapping_file">
-                  <param name="type" type="select" label="Bowtie mapping flags (Default -v 0 -a --best --strata)">
-                    <option value="default">Default</option>
-                    <option value="user">User specified</option>
-                  </param>
-                  <when value="default"/>
-                  <when value="user"> 
-                    <param name="param_v" type="integer" value="0" label="Number of mismatches for SOAP-like alignment policy (-v)"/>
-                    <param name="param_five" type="integer" value="0" label="Trim n bases from high-quality (left) end of each read before alignment (-5)"/>
-                    <param name="param_three" type="integer" value="0" label="Trim n bases from high-quality (right) end of each read before alignment (-3)"/>
-                    <param name="param_k" type="integer" value="1" label="Report up to n valid alignments per read (-k)"/>
-                    <param name="param_a" type="boolean" checked="False" truevalue = "1" falsevalue = "0" label="Whether or not to report all valid alignments per read (-a)"/>
-                    <param name="param_m" type="integer" value="-1" label="Suppress all alignments for a read if more than n reportable alignments exist (-m), -1 for unlimited"/>
-                    <param name="param_best" type="boolean" checked="False" truevalue = "1" falsevalue = "0" label="Whether or not to make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum and in terms of the quality values at the mismatched positions (--best --strata)"/>
-                  </when>
-                </conditional>
-
-	</inputs>
-	<outputs>
-		<data name="output" type="data" format="bam"/>
-	</outputs>
-
-	<help>
-
-
-**TIPS**:
-
------
-
-**Input**:
-
-* 1. Sequence file type (FASTA/FASTQ)
-* 2. Sequence file (fasta/fastq format) {Default: fastq file}
-* 3. Reference file (e.g. cDNA library [fasta])
-* 4. “Shift” (The length of the sequence that will be trimmed at the 3’end of the reads before each round of mapping)
-* 5. “Length” (The minimum length of the reads for mapping after trimming)
-* [Optional]
-* 1. Bowtie mapping flags (options) [Default: -v 0 -a --best --strata] (-v flag indicates the number of allowed mismatches. use -5/-3 flag to trim nucleotides from 5'/3' end of the reads)
-
------
-
-**Output**:
-
-A bam file with all of the reads that are mapped	
-
-
-
-	</help>
-</tool>
diff -r f4cc06e92530 -r a292aaf51735 Iterative_mapping/map_ex.py
--- a/Iterative_mapping/map_ex.py	Mon Sep 15 14:52:20 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,31 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-import sys
-from read_file import *
-from Bio import SeqIO
-
-map_file = sys.argv[1]
-result_file = sys.argv[2]
-
-
-#reads = read_t_file(read_file);
-
-f = open(map_file);
-h = file(result_file, 'w')
-
-for aline in f.readlines():
-    tline = aline.strip();
-    tl = tline.split('\t');
-    if len(tl)>4:
-        if int(tl[1].strip())== 0:
-            h.write(tline)
-            h.write('\n')
-
-
-f.close();
-h.close()
-
-
-
-
diff -r f4cc06e92530 -r a292aaf51735 Iterative_mapping/read_file.py
--- a/Iterative_mapping/read_file.py	Mon Sep 15 14:52:20 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,21 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-import sys
-
-
-
-def read_t_file(in_file):
-    f = open(in_file);
-    result = [];
-    for aline in f.readlines():
-        temp = [];
-        tline = aline.strip();
-        tl = tline.split('\t');
-        for i in range(0, len(tl)):
-            temp.append(tl[i].strip());
-        result.append(temp);
-    f.close();
-    return result;
-
-
diff -r f4cc06e92530 -r a292aaf51735 Iterative_mapping/read_s_file.py
--- a/Iterative_mapping/read_s_file.py	Mon Sep 15 14:52:20 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,22 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-import sys
-
-
-
-def read_sp_file(in_file):
-    f = open(in_file);
-    result = [];
-    for aline in f.readlines():
-        temp = [];
-        tline = aline.strip();
-        tl = tline.split(' ');
-        for i in range(0, len(tl)):
-            if len(tl[i].strip())>0:
-                temp.append(tl[i].strip());
-        result.append(temp);
-    f.close();
-    return result;
-
-
diff -r f4cc06e92530 -r a292aaf51735 Iterative_mapping/remove_map.py
--- a/Iterative_mapping/remove_map.py	Mon Sep 15 14:52:20 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,29 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-import sys
-from read_file import *
-
-
-unmap_file = sys.argv[1]
-map_file = sys.argv[2]
-result_file = sys.argv[3]
-
-
-unmap = read_t_file(unmap_file)
-mapped = read_t_file(map_file)
-h = file(result_file, 'w')
-
-maps = set()
-for i in range(len(mapped)):
-    maps.add(mapped[i][0])
-
-
-for i in range(len(unmap)):
-    name = unmap[i][0]
-    if name not in maps:
-        h.write(name)
-        h.write('\n')
-
-
-h.close()
diff -r f4cc06e92530 -r a292aaf51735 Iterative_mapping/seq_track.py
--- a/Iterative_mapping/seq_track.py	Mon Sep 15 14:52:20 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,38 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-import sys
-from read_file import *
-from Bio import SeqIO
-
-unmap_file = sys.argv[1]
-reads_file = sys.argv[2]
-result_file = sys.argv[3]
-tp = sys.argv[4]
-
-
-unmap = read_t_file(unmap_file);
-
-h = file(result_file, 'w')
-
-reads = SeqIO.parse(reads_file,tp)
-um = set()
-for i in range(0, len(unmap)):
-    id_r = unmap[i][0]
-    um.add(id_r)
-
-for read in reads:
-    if read.id in um:
-        h.write('>')
-        h.write(read.id)
-        h.write('\n')
-        h.write(read.seq.tostring())
-        h.write('\n')
-    
-
-
-h.close()
-
-
-
-
diff -r f4cc06e92530 -r a292aaf51735 Iterative_mapping/tool_dependencies.xml
--- a/Iterative_mapping/tool_dependencies.xml	Mon Sep 15 14:52:20 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,15 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="biopython" version="1.61">
-        <repository changeset_revision="ae9dda584395" name="package_biopython_1_61" owner="biopython" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="numpy" version="1.7">
-        <repository changeset_revision="ef12a3a11d5b" name="package_numpy_1_7" owner="iuc" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="samtools" version="0.1.18">
-        <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" prior_installation_required="False" 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" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>
diff -r f4cc06e92530 -r a292aaf51735 Iterative_mapping/truncate.py
--- a/Iterative_mapping/truncate.py	Mon Sep 15 14:52:20 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,32 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-import sys
-from Bio import SeqIO
-
-fasta_file = sys.argv[1]
-shift_in = sys.argv[2]
-result_file = sys.argv[3]
-length = sys.argv[4]
-
-shift = int(shift_in)
-    
-fasta_sequences = SeqIO.parse(open(fasta_file),'fasta');
-h = file(result_file,'w')
-for seq in fasta_sequences:
-        nuc = seq.id;
-        sequence = seq.seq.tostring();
-        if (len(sequence)-shift)>=int(length):
-                h.write('>'+nuc)
-                h.write('\n')
-                h.write(sequence[0:(len(sequence)-shift)])
-                h.write('\n')
-
-
-
-
-h.close()
-
-
-
-
diff -r f4cc06e92530 -r a292aaf51735 Iterative_mapping/unmap.py
--- a/Iterative_mapping/unmap.py	Mon Sep 15 14:52:20 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,31 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-import sys
-from read_file import *
-from Bio import SeqIO
-
-map_file = sys.argv[1]
-result_file = sys.argv[2]
-
-
-#reads = read_t_file(read_file);
-
-f = open(map_file);
-h = file(result_file, 'w')
-
-for aline in f.readlines():
-    tline = aline.strip();
-    tl = tline.split('\t');
-    if len(tl)>4:
-        if int(tl[1].strip()) != 0:
-            h.write(tl[0].strip());
-            h.write('\n');
-
-
-f.close();
-h.close()
-
-
-
-
diff -r f4cc06e92530 -r a292aaf51735 predict/.DS_Store
Binary file predict/.DS_Store has changed
diff -r f4cc06e92530 -r a292aaf51735 predict/parse_dis_pac.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/predict/parse_dis_pac.py	Mon Sep 15 14:52:43 2014 -0400
@@ -0,0 +1,43 @@
+#parse reactivity file into a dictionary
+
+import sys
+
+def parse_dist(in_file):
+    result = []
+    distribution = {}
+    name = []
+    f = open(in_file)
+    for aline in f.readlines():
+        line = aline.strip()
+        dis = line.strip()
+        dist = dis.split('\t') #split the line and the reactivites or reads are in a list
+        if len(dist) > 0:
+            if len(dist) == 1:
+                if dist[0].strip().find('coverage')==-1:
+                    name.append(line) #add the name in the name list
+                    flag = 1
+                    t_name = line
+            else:
+                distri = []
+                for i in range(0, len(dist)):
+                    distri.append(dist[i].strip())
+                distribution[t_name] = distri #add the list of reactivities into a dictionary
+    result.append(name)
+    result.append(distribution) #Output the dictionary
+    f.close()
+    return result
+                
+                
+
+
+
+
+
+
+
+        
+
+
+
+
+
diff -r f4cc06e92530 -r a292aaf51735 predict/predict_RNAs.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/predict/predict_RNAs.py	Mon Sep 15 14:52:43 2014 -0400
@@ -0,0 +1,93 @@
+#RNA structure prediction & Output and illustrate reactivities
+
+import sys
+from parse_dis_pac import *
+from read_file import *
+from Bio import SeqIO
+import os
+from rtts_plot import *
+
+
+id_file = sys.argv[1]
+seq_file = sys.argv[2]
+output_file = sys.argv[4]
+
+
+flag = 0
+if sys.argv[3]!='None': #input reactivity file if provided
+    react_file = sys.argv[3]
+    react = parse_dist(react_file)
+    react = react[1]
+    flag = 1
+
+ospath = os.path.realpath(sys.argv[0])
+ost = ospath.split('/')
+syspath = ""
+for i in range(len(ost)-1):
+    syspath = syspath+ost[i].strip()
+    syspath = syspath+'/' 
+
+ids = read_t_file(id_file)
+sequences = SeqIO.parse(seq_file, 'fasta')
+
+
+seqs = {}
+for seq in sequences:
+    seqs[seq.id] = seq.seq.tostring()
+
+if len(ids)>10: #setup a limit of the number of sequence to be predicted
+    print("Number of sequences exceeds limitation!")
+    sys.exit(0)
+    
+
+#predict RNA structures
+os.system("mkdir "+syspath+"output_f")
+for i in range(len(ids)):
+    id_s = ids[i][0]
+    print(id_s)
+    #Put RNA sequence and reactivities into files
+    if id_s in seqs:
+        f = file(syspath+"temp.txt", 'w')        
+        f.write('>'+id_s)
+        f.write('\n')
+        f.write(seqs[id_s])
+        f.close()
+        if flag == 0:
+            os.system("Fold "+syspath+"temp.txt"+" "+syspath+"output_f/"+id_s+".ct")
+        if flag == 1:
+            if id_s in react:
+                f = file(syspath+"constraint.txt",'w')
+                make_plot(react[id_s],id_s,(syspath+"output_f/")) #make a plot of the distribution of the reactivites of the input RNA
+                #h = file(syspath+"output_f/transcript_reactivities.txt", 'w')
+                #h.write(id_s)
+                #h.write('\n')
+                for j in range(0, (len(react[id_s]))):
+                    if react[id_s][j]!='NA':
+                        f.write(str(j+1))
+                        f.write('\t')
+                        f.write(str(react[id_s][j]))
+                        f.write('\n')
+                    #h.write(str(react[id_s][j])) #Output the reactivities
+                    #h.write('\t')
+                f.close()
+                #h.write('\n')
+                #h.write('\n')
+                os.system("Fold "+syspath+"temp.txt"+" -sh"+" "+syspath+"constraint.txt"+" "+syspath+"output_f/"+id_s+".ct")
+            else:
+                print(id_s+" not in the data of react!")
+        os.system("draw "+syspath+"output_f/"+id_s+".ct "+syspath+"output_f/"+id_s+".ps")
+    else:
+        print(id_s+" not in the data of sequences!")
+
+#Remove the unnecessary files
+os.system("tar -zcvPf "+output_file+" "+syspath+"output_f/"+"*.*")
+os.system("rm -f "+syspath+"temp.txt")
+os.system("rm -r "+syspath+"output_f")
+if flag == 1:
+    os.system("rm -f "+syspath+"constraint.txt")
+ #   h.close()
+    
+    
+
+
+
diff -r f4cc06e92530 -r a292aaf51735 predict/predict_RNAs.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/predict/predict_RNAs.xml	Mon Sep 15 14:52:43 2014 -0400
@@ -0,0 +1,63 @@
+<tool id="predict_pipeline" name="RNA structure prediction" version="1.0">
+	<description></description>
+	<command interpreter="python">predict_RNAs.py $rna_list $reference_file $reactivity_file $output </command>
+        <requirements>
+                <requirement type="package" version="1.61">biopython</requirement>
+                <requirement type="package" version="1.7">numpy</requirement>
+        </requirements>
+	<inputs>
+        <param name="rna_list" type="data" format="txt" label="List of RNA ids to predict"/>
+        <param name="reference_file" type="data" format="fasta" label="Reference genome/transcriptome"/>
+        <param name="reactivity_file" type="data" optional = "true" label="Reactivity"/>
+<!---
+        <conditional name="reactivity">
+            <param name="choose" type="select" label="Reactivity files exists?">
+                <option value="N">No</option>
+                <option value="Y">Yes</option>
+            </param>
+            <when value="Y">
+                <param name="reactivity_file" type="data" optional = "true" label="Reactivity"/>
+            </when>
+            <when value="N"/>
+        </conditional>  
+
+-->		
+	</inputs>
+	<outputs>
+		<data name="output" format=".tgz"/>
+	</outputs>
+
+	<help>
+
+
+**TIPS**:
+
+-----
+
+**Input**:
+
+* 1. A file with transcript Ids (Max num. 20), (each ID one line)
+* 2. Reference file (fasta) used to map the reads
+* [Optional]:
+* 1. A reactivity file with structural reactivity for each nucleotide on the sequence provided
+
+-----
+
+**Output**:
+
+* 1. .ct files with predicted RNA structures [transciptID.ct]
+* 2. .ps files which depict the predicted RNA structures [[transciptID.ps]
+* [Optional]
+* 3. .png files that shows the distribution of the reactivity of each nucleotide on the transcripts of interest. [transciptID.png]
+* 4. A .txt file that includes the reactivities of all the nucleotides on the transcripts of interest. [transciptID.txt]
+
+-----
+
+**Attention**
+
+Make sure any of the transcript Ids does not contain "|" or space!	
+
+
+
+	</help>
+</tool>
diff -r f4cc06e92530 -r a292aaf51735 predict/rRNA.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/predict/rRNA.txt	Mon Sep 15 14:52:43 2014 -0400
@@ -0,0 +1,8 @@
+>25s rRNA 3375nts
+GCGACCCCAGGTCAGGCGGGATTACCCGCTGAGTTTAAGCATATCAATAAGCGGAGGAAAAGAAACTAACAAGGATTCCCTTAGTAACGGCGAGCGAACCGGGAAGAGCCCAGCTTGAAAATCGGACGTCTTCGGCGTTCGAATTGTAGTCTGGAGAAGCGTCCTCAGCGACGGACCGGGCCTAAGTTCCCTGGAAAGGGGCGCCAGAGAGGGTGAGAGCCCGTCGTGCCCGGACCCTGTCGCACCACGAGGCGCTGTCTACGAGTCGGGTTGTTTGGGAATGCAGCCCCAATCGGGCGGTAAATTCCGTCCAAGGCTAAATACGGGCGAGAGACCGATAGCGAACAAGTACCGCGAGGTAAAGATGAAAAGGACTTTGAAAAGAGAGTCAAAGAGTGCTTGAAATTGTCGGGAGGGAAGCGGATGGGGGCCGGCGATGCGTCCTGGTCGGATGCGGAACGGAGCAATCCGGTCCGCCGATCGATTCGGGGCGTGGACCGACGCGGATTACGGTGGCGGCCTAAGCCCGGGCTTTTGATACGCTTGTGGAGACGTCGCTGCCGTGATCGTGGTCTGCAGCACGCGCCTAACGGCGTGCCTCGGCATCAGCGTGCTCCGGGCGTCGGCCTGTGGGCTCCCCATTCGACCCGTCTTGAAACACGGACCAAGGAGTCTGACATGTGTGCGAGTCAACGGGTGAGTAAACCCGTAAGGCGCAAGGAAGCTGATTGGCGGGATCCTCGCGGGTGCACCGCCGACCGACCTTGATCTTCTGAGAAGGGTTCGAGTGTGAGCATGCCTGTCGGGACCCGAAAGATGGTGAACTATGCCTGAGCGGGGTAAAGCCAGAGGAAACTCTGGTGGAAGCCCGCAGCGATACTGACGTGCAAATCGTTCGTCTGACTTGGGTATAGGGGCGAAAGACTAATCGAACCATCTAGTAGCTGGTTCCCTCCGAAGTTTCCCTCAGGATAGCTGGAGCTCGGACGCGAGTTCTATCGGGTAAAGCCAATGATTAGAGGCATTGGGGGCGCAACGCCTCGACCTATTCTCAAACTTTAAATAGGTAGGACGTGTCGGCTGCTTTGTTGAGCCGTCACACGGAATCGAGAGCTCCAAGTGGGCCATTTTTGGTAAGCAGAACTGGCGATGCGGGATGAACCGGAAGCCGGGTTACGGTGCCCAACTGCGCGCTAACCTAGAACCCACAAAGGGTGTTGGTCGATTAAGACAGCAGGACGGTGGTCATGGAAGTCGAAATCCGCTAAGGAGTGTGTAACAACTCACCTGCCGAATCAACTAGCCCCGAAAATGGATGGCGCTTAAGCGCGACCTATACCCGGCCGTCGGGGCAAGAGCCAGGCCTCGATGAGTAGGAGGGCGCGGCGGTCGCTGCAAAACCTAGGGCGCGAGGCGCGGAGCGGCCGTCGGTGCAGATCTTGGTGGTAGTAGCAAATATTCAAATGAGAACTTTGAAGGCCGAAGAGGGGAAAGGTTCCATGTGAACGGCACTTGCACATGGGTTAGTCGATCCTAAGAGTCGGGGGAAACCCGTCTGATAGCGCTTAAGCGAACTTCGAAAGGGGATCCGGTTAAAATTCCGGAACCGGGACGTGGCGGTTGACGGCAACGTTAGGGAGTCCGGAGACGTCGGCGGGGGCCTCGGGAAGAGTTATCTTTTCTGTTTAACAGCCTGCCCACCCTGGAAACGGCTCAGCCGGAGGTAGGGTCCAGCGGCTGGAAGAGCACCGCACGTCGCGTGGTGTCCGGTGCGCCCCCGGGCGCCCTTGAAAATCCGGAGGACCGAGTGCCGCTCACGCCCGGTCGTACTCATAACCGCATCAGGTCTCCAAGGTGAACAGCCTCTGGTCGATGGAACAATGTAGGCAAGGGAAGTCGGCAAAATGGATCCGTAACTTCGGGAAAAGGATTGGCTCTGAGGGCTGGGCTCGGGGGTCCCAGTTCCGAACCCGTCGGCTGTCAGCGGACTGCTCGAGCTGCTTCCGCGGCGAGAGCGGGTCGCCGGCTGCCGGCCGGGGGACGACTGGGAACGGCTCTCTCGGGAGCTTTCCCCGGGCGTCGAACAGTCAGCTCAGAACTGGTACGGACAAGGGGAATCCGACTGTTTAATTAAAACAAAGCATTGCGATGGTCCCTGCGGATGCTAACGCAATGTGATTTCTGCCCAGTGCTCTGAATGTCAAAGTGAAGAAATTCAACCAAGCGCGGGTAAACGGCGGGAGTAACTATGACTCTCTTAAGGTAGCCAAATGCCTCGTCATCTAATTAGTGACGCGCATGAATGGATTAACGAGATTCCCACTGTCCCTGTCTACTATCCAGCGAAACCACAGCCAAGGGAACGGGCTTGGCAGAATCAGCGGGGAAAGAAGACCCTGTTGAGCTTGACTCTAGTCCGACTTTGTGAAATGACTTGAGAGGTGTAGGATAAGTGGGAGCTTCGGCGCAAGTGAAATACCACTACTTTTAACGTTATTTTACTTACTCCGTGAATCGGAGGCCGGGGTACAACCCCTGTTTTTGGTCCCAAGGCTCGCTTCGGCGGGTCGATCCGGGCGGAGGACATTGTCAGGTGGGGAGTTTGGCTGGGGCGGCACATCTGTTAAAAGATAACGCAGGTGTCCTAAGATGAGCTCAACGAGAACAGAAATCTCGTGTGGAACAAAAGGGTAAAAGCTCGTTTGATTCTGATTTTCAGTACGAATACGAACCGTGAAAGCGTGGCCTATCGATCCTTTAGACTTCGGAATTTGAAGCTAGAGGTGTCAGAAAAGTTACCACAGGGATAACTGGCTTGTGGCAGCCAAGCGTTCATAGCGACGTTGCTTTTTGATCCTTCGATGTCGGCTCTTCCTATCATTGTGAAGCAGAATTCACCAAGTGTTGGATTGTTCACCCACCAATAGGGAACGTGAGCTGGGTTTAGACCGTCGTGAGACAGGTTAGTTTTACCCTACTGATGCCCGCGTCGCGATAGTAATTCAACCTAGTACGAGAGGAACCGTTGATTCGCACAATTGGTCATCGCGCTTGGTTGAAAAGCCAGTGGCGCGAAGCTACCGTGCGCTGGATTATGACTGAACGCCTCTAAGTCAGAATCCGGGCTAGAAGCGACGCATGCGCCCGCCGCCCGATTGCCGACCCTCAGTAGGAGCTTAGGCTCCAAAGGCACGTGTCGTTGGCTAAGTCCGTTCGGCGGAACGGTCGTTCGGACCGCCTTGAATTATAATTACCACCGAGCGGCGGGTAGAATCCTTTGCAGACGACTTAAATACGCGACGGGGTATTGTAAGTGGCAGAGTGGCCTTGCTGCCACGATCCACTGAGATTCAGCCCTTTGTCGCTAAGATTCGA
+>gi|20197903:2706-4513 Arabidopsis thaliana chromosome 2 BAC F23H14 genomic sequence, complete sequence
+TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGTAAGTATGAACGAATTCAGACTGTGAAACTGCGAATGGCTCATTAAATCAGTTATAGTTTGTTTGATGGTAACTACTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACAAACCCCGACTTATGGAAGGGACGCATTTATTAGATAAAAGGTCGACGCGGGCTCTGCCCGTTGCTCTGATGATTCATGATAACTCGACGGATCGCATGGCCTCTGTGCTGGCGACGCATCATTCAAATTTCTGCCCTATCAACTTTCGATGGTAGGATAGTGGCCTACCATGGTGGTAACGGGTGACGGAGAATTAGGGTTCGATTCCGGAGAGGGAGCCTGAGAAACGGCTACCACATCCAAGGAAGGCAGCAGGCGCGCAAATTACCCAATCCTGACACGGGGAGGTAGTGACAATAAATAACAATACTGGGCTCTTTCGAGTCTGGTAATTGGAATGAGTACAATCTAAATCCCTTAACGAGGATCCATTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATATTTAAGTTGTTGCAGTTAAAAAGCTCGTAGTTGAACCTTGGGATGGGTCGGCCGGTCCGCCTTTGGTGTGCATTGGTCGGCTTGTCCCTTCGGTCGGCGATACGCTCCTGGTCTTAATTGGCCGGGTCGTGCCTCCGGCGCTGTTACTTTGAAGAAATTAGAGTGCTCAAAGCAAGCCTACGCTCTGGATACATTAGCATGGGATAACATCATAGGATTTCGATCCTATTGTGTTGGCCTTCGGGATCGGAGTAATGATTAACAGGGACAGTCGGGGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGATTTATGAAAGACGAACAACTGCGAAAGCATTTGCCAAGGATGTTTTCATTAATCAAGAACGAAAGTTGGGGGCTCGAAGACGATCAGATACCGTCCTAGTCTCAACCATAAACGATGCCGACCAGGGATCAGCGGATGTTGCTTATAGGACTCCGCTGGCACCTTATGAGAAATCAAAGTTTTTGGGTTCCGGGGGGAGTATGGTCGCAAGGCTGAAACTTAAAGGAATTGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACTCAACACGGGGAAACTTACCAGGTCCAGACATAGTAAGGATTGACAGACTGAGAGCTCTTTCTTGATTCTATGGGTGGTGGTGCATGGCCGTTCTTAGTTGGTGGAGCGATTTGTCTGGTTAATTCCGTTAATGAACGAGACCTCAGCCTGCTAACTAGCTACGTGGAGGCATCCCTTCACGGCCGGCTTCTTAGAGGGACTATGGCCGTTTAGGCCAAGGAAGTTTGAGGCAATAACAGGTCTGTGATGCCCTTAGATGTTCTGGGCCGCACGCGCGCTACACTGATGTATTCAACGAGTTCACACCTTGGCCGACAGGCCCGGGTAATCTTTGAAATTTCATCGTGATGGGGATAGATCATTGCAATTGTTGGTCTTCAACGAGGAATTCCTAGTAAGCGCGAGTCATCAGCTCGCGTTGACTACGTCCCTGCCCTTTGTACACACCGCCCGTCGCTCCTACCGATTGAATGATCCGGTGAAGTGTTCGGATCGCGGCGACGTGGGTGGTTCGCCGCCCGCGACGTCGCGAGAAGTCCACTAAACCTTATCATTTAGAGGAAGGAGAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTG
+>Arabidopsis thaliana 1
+GGATGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCATCCCTC
+>gi|186498419|ref|NR_022453.1| Arabidopsis thaliana (AT2G01020) rRNA
+AAAACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCCAAGCCTTCTGGCCGAGGGCACGTCTGCCTGGGTGTCACAA
\ No newline at end of file
diff -r f4cc06e92530 -r a292aaf51735 predict/rRNA_react.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/predict/rRNA_react.txt	Mon Sep 15 14:52:43 2014 -0400
@@ -0,0 +1,8 @@
+gi|186498419|ref|NR_022453.1|
+0.0349942738544	0.219596062195	0.0958706408233	0.194395004716	0.165304592733	NA	0.649363521545	0.004703371147	NA	0.0	NA	0.0	NA	NA	0.226052814765	0.145104959196	0.235114323931	0.590973505942	NA	NA	0.671823965086	NA	0.600180467352	NA	0.0	NA	0.67204697444	NA	NA	0.0	NA	0.0	NA	0.0	NA	0.0	0.0905633447413	NA	0.0844580185128	NA	0.0	NA	NA	0.387056722073	0.063190678881	NA	0.302648296659	0.123623615737	0.0	NA	NA	0.288529445998	NA	0.0	NA	0.272682267617	1.18142319227	0.222698183429	NA	NA	0.0	NA	0.308507027145	NA	0.0	0.0	NA	NA	NA	NA	NA	NA	NA	NA	1.09905990052	0.331081493258	NA	NA	NA	0.0	0.316741455	NA	0.152869347497	0.358830282006	NA	0.172524825658	0.0232297542077	0.397612802938	NA	NA	NA	0.591410529537	0.531312624449	0.0105725487651	0.0	0.544371401206	NA	0.764412925075	NA	1.31480559071	NA	NA	0.338476420086	NA	NA	NA	NA	0.315926121887	0.0	0.0	NA	0.0	0.708180867703	1.4961467391	NA	NA	NA	NA	0.664465128059	NA	0.0	0.0	0.562535200045	0.476678390556	2.19691885985	0.524311802546	NA	1.61857603596	0.0	NA	NA	0.0	NA	NA	NA	0.0	0.0	NA	1.46994373288	NA	NA	NA	0.0	0.0	0.0	NA	NA	0.0	NA	NA	0.0	0.0	NA	NA	NA	NA	NA	NA	NA	0.0	0.0	0.0	0.0
+25s
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A	0.167954420125	0.0	0.0	NA	0.0	NA	1.25963308137	1.65490763074	0.349665039522	0.0	0.0	0.0	0.0	0.088135396391	NA	0.0	0.0	0.052063263328	1.10030351945	NA	NA	NA	0.0	0.0	0.0	NA	NA	NA	0.0	NA	NA	NA	NA	0.0	1.19282107102	NA	0.351500033721	0.0	NA	0.0	0.0	NA	0.0	NA	NA	NA	NA	0.639486692424	1.72246658214	1.27928669427	NA	1.79434484187	1.43487503629	NA	1.11459423067	1.28050635355	0.0	0.033808248598	NA	NA	NA	NA	NA	0.0	NA	0.0	NA	NA	NA	0.037351845069	0.0	NA	0.0	NA	0.0	NA	NA	0.0	0.0	NA	0.0680509646718	0.0	NA	NA	NA	NA	NA	NA	0.216734779888	0.238453108898	0.0047777392186	NA	NA	0.0	0.0	NA	NA	NA	0.24091195962	NA	0.367136308324	NA	NA	NA	NA	NA	0.0364529921341	NA	NA	0.290430964122	NA	0.0292200666431	0.0	NA	NA	NA	NA	NA	0.0	NA	0.0	NA	NA	0.376846428488	NA	NA	0.0538172630509	NA	0.478261010535	0.721287586992	0.582408590163	NA	NA	NA	0.41727516366	0.401127778986	0.723354419621	NA	0.095607199307	0.258806359595	0.0835986123205	0.0	0.0	NA	0.0	0.0	NA	NA	NA	NA	0.440304834094	0.265761431623	0.519660229692	NA	NA	NA	0.168302233778	NA	NA	NA	NA	0.157327271761	0.0	NA	NA	0.0	0.0	NA	0.0	0.0	NA	NA	NA	0.0924344002851	0.0	NA	0.0	NA	NA	0.375769028351	NA	NA	0.0446187487194	0.0	NA	NA	NA	NA	NA	0.516864204729	0.172416681072	0.0567192634098	0.0378721224169	0.00299445087817	0.0932354718163	0.0743292528517	0.0912629153496	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	0.992289703074	0.0	0.316404114911	0.107107875064	0.520226987768	NA	NA	0.0	NA	0.361658745396	NA	0.0	NA	NA	0.651767453937	NA	NA	0.373975972699	NA	NA	NA	NA	0.0	NA	1.38394570998	NA	0.0	1.00495180372	NA	NA	NA	0.284672456867	NA	NA	0.0	NA	NA	0.431826210178	0.0	0.0	NA	NA	NA	NA	0.0	0.0901844111313	NA	NA	NA	NA	NA	NA	NA	0.0	NA	NA	NA	NA	NA	NA	0.0	NA	NA	NA	NA	NA	1.33336901534	NA	NA	0.191191895748	1.4841175405	0.392189953008	1.45736007574	NA	0.311778885904	NA	NA	NA	NA	0.176831354715	0.673338414422	0.0443852672859	0.0929438936537	NA	0.0	NA	0.0	0.0	0.0	NA	0.0	0.0694646091221	NA	NA	NA	NA	NA	0.0	0.0	NA	0.192693932018	0.288541449812	NA	0.475655710856	NA	NA	0.388660038013	NA	0.00984462464751	NA	0.0	1.81119542895	1.58177307546	0.571881702456	NA	0.841799847816	NA	0.0	1.8803751819	1.55005205033	0.817218685186	NA	1.88597635494	1.3912539199	1.62016777444	NA	0.218813430261	NA	0.209125600132	NA	NA	NA	NA	NA	NA	0.00152129255625	0.0692149342689	0.482781374021	0.286646187881	0.116245486156	0.258681032169	0.0426374923982	NA	NA	NA	NA	1.19938393364	0.632277359129	0.551425712127	0.824991309934	NA	0.00546462277811	NA	0.0	NA	NA	NA	NA	NA	0.190663657047	NA	NA	0.0552614588428	NA	NA	0.340937408688	NA	NA	NA	NA	0.13847541988	0.20559094886	NA	NA	0.781555754406	0.0	NA	0.525171284317	0.436527075283	NA	0.0421028137972	0.0307349474561	NA	0.281933713892	0.0	0.629440274879	0.179786036677	NA	NA	NA	0.11835642342	0.198474100584	0.261444284574	NA	0.0	NA	NA	NA	NA	0.0	0.0	NA	0.26387724218	NA	0.0	NA	0.472854357389	NA	1.74976904497	0.87854869935	NA	NA	NA	0.0	NA	0.151450492281	0.0	NA	NA	0.0	NA	NA	0.351662153841	0.0	NA	NA	NA	NA	0.0701877141513	0.429452307682	NA	0.0	NA	0.0	NA	0.0	NA	NA	NA	NA	NA	0.0	0.0	NA	0.0	0.0	0.0	0.0	NA	NA	NA	0.0533163327192	0.0	0.0	0.0	0.0	0.0	NA	NA	NA	0.508254834906	NA	0.0	0.0	0.0	NA	NA	NA	0.0	NA	NA	NA	NA	NA	NA	0.0	0.0	NA	0.0	0.0	0.0	0.853405247499	NA	0.0	NA	NA	NA	0.0	0.0	NA	0.800049449505	NA	0.0	NA	0.0381971897849	0.0	NA	NA	NA	NA	0.0	NA	NA	NA	NA	NA	NA	0.0	NA	0.0	0.0	NA	NA	0.0	NA	0.653339817705	NA	NA	NA	0.0	NA	NA	0.0	NA	0.0	NA	NA	0.0	0.0	NA	0.0	NA	0.0	0.0	NA	NA	NA	NA	NA	0.0	0.0	NA	0.0	0.0	NA	0.678467855295	0.0	NA	NA	0.0	0.0	0.0	0.0	0.0	0.0	NA	NA	NA	NA	NA	NA	NA	0.0	NA	NA	NA	NA	NA	0.0	0.0	0.0	0.0	0.0	0.018664182086	0.0	0.0	0.0	0.0	NA	0.0	NA	NA	NA	0.0	0.121678706886	0.355299241427	NA	NA	NA	1.73293458871	NA	0.0493727138012	NA	NA	NA	NA	NA	NA	NA	0.0568785504168	NA	0.134312284659	0.0	0.0	NA	NA	0.0	NA	NA	NA	0.433579288967	NA	0.445397859363	0.0	0.975058935559	NA	NA	NA	NA	0.334019900058	NA	NA	NA	NA	NA	0.819899325822	0.0	0.0	0.0	NA	0.0	0.0	NA	NA	0.0	NA	NA	0.14790191642	0.355048973175	0.632457142469	NA	0.0885424973481	NA	NA	0.0	NA	0.245308306361	NA	1.45476259015	NA	0.461488242458	NA	NA	0.0403145742559	0.0669040008976	NA	NA	0.189059523364	0.223383021291	0.443345417968	0.302699986613	0.261935974538	NA	0.453463826854	NA	NA	0.281780796046	0.0	NA	0.222728714314	NA	0.496511941732	NA	NA	0.648092143251	0.867025205093	0.698984683105	0.342390556037	NA	NA	NA	NA	0.0	NA	NA	0.0	NA	0.0	0.0	0.0	0.8816043907	0.0	NA	NA	NA	NA	NA	0.0	0.0	NA	0.0	NA	0.143927736109	NA	0.0	NA	NA	NA	NA	NA	NA	NA	0.0	0.643731475471	1.04357444649	0.662993815823	NA	0.0	0.0461426678103	0.0	NA	NA	NA	NA	0.0	NA	0.0	NA	0.0	0.033505630595	NA	0.0	NA	0.133469644664	0.0	0.234879130863	NA	NA	NA	0.0	NA	0.0	NA	NA	NA	0.688130547851	NA	NA	0.732542656381	NA	NA	0.0	0.0	NA	NA	0.438119294374	0.558376720682	0.0	NA	0.918102306041	0.56240697358	NA	0.0	NA	0.237088351477	0.0	NA	NA	0.0	0.20233663462	NA	0.600412306412	0.183536339486	NA	0.0	0.0	NA	NA	NA	0.0	NA	0.0	NA	0.732387193297	0.63658249172	NA	0.010121757995	NA	0.0	0.0	NA	0.0	0.641739077143	NA	NA	0.0731629955416	NA	0.0	0.0	0.0	NA	0.0	0.0	NA	0.0	0.0	0.0	NA	0.0	NA	NA	NA	0.0	0.0	NA	0.0	0.0	0.0	0.0	NA	0.0	0.0	NA	NA	0.389549029322	NA	NA	0.0	NA	0.472854357389	NA	NA	0.0	NA	NA	0.0	NA	0.0	0.0	0.0	0.0	0.37028839264	NA	NA	0.0	0.0481524671794	0.387465196563	NA	NA	NA	NA	0.0	NA	NA	NA	NA	NA	0.0	NA	0.640486051737	0.354013107665	NA	NA	0.337971646441	0.0	NA	NA	NA	0.0	NA	NA	0.0	NA	NA	0.447020729153	0.309541139682	0.0	NA	NA	NA	0.686037910468	NA	NA	NA	0.3406752016	NA	NA	0.146691758883	0.0	0.0	NA	0.0	0.0	NA	NA	NA	0.913095760914	1.03984524992	NA	NA	0.868123808953	NA	0.273507880758	0.0	NA	NA	0.0	0.0562709433796	0.0	0.117755450683	1.09301118286	0.3406752016	NA	0.279937783278	NA	0.472854357389	NA	NA	0.0	NA	NA	NA	NA	1.1279640247	NA	2.021448478	0.0	NA	0.940786080429	1.03814311506	NA	NA	NA	NA	0.844770381547	0.661304456557	NA	0.741654233914	0.0	NA	0.0975430676565	0.0437438686722	NA	NA	0.594144441129	0.350319089768	1.93721008621	NA	1.22231078215	0.0	NA	0.0	NA	0.0	0.538436231703	NA	NA	NA	NA	NA	0.0	NA	NA	NA	NA	0.0508327001275	0.279131420348	NA	NA	NA	NA	0.0	0.109423953351	NA	0.0	NA	NA	NA	NA	0.271679433027	0.0	NA	NA	NA	0.0	NA	NA	0.0	0.0	0.0	0.46793172304	NA	0.0	NA	0.0	0.0	0.0	0.0	NA	NA	0.749456424764	NA	0.0	NA	NA	0.472854357389	1.22231078215	NA	0.0	0.0	0.0	NA	NA	NA	NA	NA	0.0	NA	0.0	NA	0.0	0.0	NA	0.0	NA	NA	0.0	NA
+Arabidopsis
+NA	NA	0.0	NA	NA	3.53700365182	NA	0.0	NA	0.0	0.0	NA	0.0	0.0	0.0	5.10017382764	NA	0.0	0.0	0.0	NA	0.0	0.0	NA	NA	0.0	0.0	0.0	0.0	NA	NA	0.0	NA	0.0	0.0	0.0	1.04740785071	NA	0.751507319045	0.679065423588	NA	0.0	1.80093151001	0.0	NA	0.0	0.0	NA	0.0	0.0	NA	NA	NA	0.0	0.0	NA	2.35404575646	NA	NA	NA	4.93385220878	NA	NA	NA	NA	NA	0.0	NA	0.0	NA	4.45571252703	NA	NA	0.0	NA	NA	0.0	0.0	NA	0.0	NA	NA	0.0	NA	NA	NA	NA	NA	NA	4.93385220878	0.0	0.0	NA	0.0	0.0	NA	NA	NA	NA	0.0	0.0	NA	NA	0.0	0.0	NA	0.0	NA	NA	NA	NA	NA	NA	0.0	0.0	NA	0.0	0.0	0.0	NA
+gi|20197903:2706-4513
+NA	0.012685795205	0.0	0.0	NA	NA	NA	NA	NA	NA	0.369865767367	NA	0.0	0.0	NA	NA	0.0	0.0	0.0	NA	NA	0.291074839291	NA	NA	0.0	0.0779489717102	NA	0.0	NA	NA	0.0	NA	NA	NA	NA	0.0	NA	0.388739681544	0.607358801578	0.86505141743	0.419532419715	NA	0.775525397956	NA	NA	0.418634405395	0.310232647615	NA	0.0	0.0	0.51629506558	NA	NA	0.0	0.435316902631	NA	NA	NA	NA	NA	0.406071541412	0.102260948087	NA	NA	1.02827139604	NA	NA	0.555559168062	0.301220165622	0.0	NA	0.428351005927	0.0	NA	NA	0.0942381418988	0.340249958839	NA	0.402129377649	0.639234686516	NA	NA	NA	NA	0.935138133481	0.0592665799408	0.143289116981	0.0473507766862	NA	NA	0.0	NA	0.0266155577151	0.0982764742903	NA	NA	NA	0.0	NA	0.0	0.11309561083	NA	NA	0.628690973329	0.479906074642	0.102631619096	NA	0.0	0.434378189774	NA	NA	NA	0.0807132307206	NA	0.0	NA	NA	NA	NA	NA	NA	NA	NA	NA	0.359209156119	NA	NA	NA	NA	0.648363725715	1.00111919062	1.04262692243	NA	0.755897037378	0.819932067068	NA	0.455162779021	1.20773264872	NA	0.0	NA	NA	0.296441851982	NA	0.37547834061	0.357493014857	0.0258046929258	0.0	NA	NA	0.505600332852	NA	NA	0.215493760216	0.137308939841	NA	NA	0.0	NA	0.327508086131	NA	0.0	NA	0.0	NA	0.110060629173	0.144925722316	NA	0.181195205113	0.198697622929	NA	NA	NA	0.430508890438	0.615380473507	0.413085955445	0.213399108191	0.970869271469	0.940875618616	0.816055880816	0.400666932367	0.0	0.0368366876912	0.0	NA	0.982940202181	0.0152093127598	NA	NA	0.772061687224	NA	NA	NA	0.524486960169	1.14258931334	NA	NA	NA	0.772909687503	0.350161317332	NA	0.0	0.339428903455	NA	NA	NA	0.289638535352	NA	NA	0.301380368516	NA	0.186709719344	NA	0.723493077315	0.549043071946	0.368933272512	0.346567668516	NA	NA	NA	0.0736517765796	NA	0.225216490874	0.0	NA	0.0	NA	NA	NA	0.282065581517	NA	0.0622206275738	NA	NA	0.0	0.0	0.0	NA	NA	NA	NA	0.0979798698289	NA	0.418716246672	NA	NA	0.127229218645	NA	NA	0.122048875919	NA	NA	0.0	0.459466284108	NA	NA	0.22611651355	NA	0.257988938793	0.242043547687	0.0445554892629	NA	0.0	NA	0.211377998276	0.0539458902463	NA	NA	0.705263055871	NA	0.122896017727	NA	0.0	0.364816537092	NA	NA	NA	0.0	0.0	NA	0.0	NA	NA	NA	NA	0.0	NA	NA	NA	0.134627940359	NA	0.384818842789	0.0	NA	0.0	0.298065186972	NA	0.0	0.148933065236	NA	NA	0.108571364914	0.245360133204	0.412047373188	0.0776738288945	NA	NA	NA	0.0	NA	NA	0.385371255467	0.0134780068585	0.186653352588	NA	0.670459919659	NA	0.0	0.163864042171	0.13720252139	0.0	NA	NA	NA	0.0	NA	0.0	NA	NA	NA	NA	0.0	NA	NA	0.0478979106433	NA	0.0	NA	NA	NA	NA	0.0	0.0	NA	0.0	0.0	0.0	0.215656364652	NA	NA	NA	NA	NA	NA	NA	0.676399501898	0.444238412823	0.0	NA	NA	NA	NA	NA	0.402502781349	0.324546337434	NA	NA	0.72428064676	NA	0.365349818072	0.282000801415	NA	NA	0.825136824379	NA	NA	NA	NA	NA	0.0	NA	0.285295564149	NA	NA	0.215476057191	0.182212745127	NA	NA	0.146330023967	NA	0.421564261825	NA	NA	NA	0.353084055047	NA	0.0	0.0	NA	NA	0.0	NA	0.236357075379	0.0	0.244357718994	0.128121995322	NA	NA	0.175198188965	NA	0.218494857155	0.0	0.0	0.00451933044375	0.0	0.927212739519	NA	0.132103213724	0.0	0.740927800969	0.957180040116	NA	NA	0.656796842311	0.580572417551	NA	NA	0.0	0.0	NA	0.0	0.0563230505075	NA	NA	0.120005485202	NA	0.226509753369	NA	0.0	0.471160925233	0.0877285693903	0.768176413935	NA	NA	0.235484190643	0.0	0.0	0.118062685793	0.419161295576	0.135347828419	NA	0.219059490441	0.426910429649	NA	NA	0.971233728998	0.0	0.0	0.48732449835	NA	NA	NA	NA	0.24138759394	NA	NA	NA	0.253899493465	NA	NA	NA	0.825841393383	0.82831906089	0.0	0.0717935208264	NA	0.279778367449	0.282811723237	0.229633772945	NA	0.0	0.0	0.0	0.509924844919	0.429039400771	NA	0.283392930386	0.0	NA	NA	NA	NA	0.0	NA	0.0	NA	NA	NA	0.117058667345	NA	0.0	NA	NA	0.0	NA	NA	NA	NA	0.0965635309754	0.092863243134	NA	NA	NA	NA	1.04941610567	1.19161444221	NA	NA	1.7376246406	NA	NA	0.391195828095	0.375473658421	0.433647125904	0.279359521091	NA	0.501405696729	NA	0.687660733308	0.864175250339	0.79158652207	NA	1.20320006049	0.56311253719	0.253888387685	NA	NA	1.83397160852	1.53706044242	0.961584043251	NA	0.784802938308	NA	NA	1.28330857645	NA	0.268894203299	0.314451464739	0.423300010695	NA	NA	NA	NA	0.259483681982	NA	NA	NA	1.26295217444	0.661502700034	0.652566369353	NA	NA	0.500429839944	NA	NA	NA	NA	NA	0.103898205626	0.255468262008	0.163276078797	NA	0.48540533193	0.395593446683	NA	0.2174452409	0.101616378857	NA	0.205131663835	NA	NA	NA	1.31997685379	0.753084647947	NA	NA	0.0519500996846	0.387428790866	0.34011021097	NA	0.0748065258161	NA	0.0580149462222	0.0768278927631	0.158589807897	0.25491474666	NA	0.347714135251	NA	0.11241524085	NA	NA	0.336941565822	NA	0.0887724160932	NA	NA	NA	0.916896362256	0.278780105213	NA	NA	NA	NA	NA	NA	NA	0.115173560016	0.31061772735	NA	NA	NA	0.486301566768	0.347179567168	0.617356828937	0.444803810174	0.408511448093	NA	0.0782866766856	NA	0.0	NA	NA	0.515740275652	NA	NA	NA	NA	0.61541889439	0.97298662914	0.462906210807	0.542827568418	NA	NA	NA	NA	NA	0.694038563065	NA	NA	NA	NA	NA	0.109092812624	NA	NA	0.0	0.117730829926	NA	NA	NA	0.134948233631	0.152419220299	NA	0.0511684766977	0.0	NA	NA	NA	NA	NA	NA	NA	NA	NA	0.445995841454	0.47369948038	NA	NA	NA	NA	NA	0.040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38202643	NA	NA	0.0	0.0	0.0356275913231	NA	NA	NA	NA	0.219870784412	0.16181267273	NA	0.0254540277981	NA	NA	NA	NA	0.0136899888528	0.0	0.0	NA	NA	NA	0.0	0.0	NA	0.0	NA	NA	NA	0.124832560383	NA	NA	NA	NA	NA	0.291168607862	NA	0.0	NA	0.0	NA	0.0	0.0	NA	NA	NA	0.0	0.0927979100847	0.300974630983	NA	NA	NA	NA	NA	NA	NA	NA	0.0	NA	NA	0.0704858304923	0.0	0.0	0.0	NA	0.0	NA	NA	0.0835696851504	0.0518565943435	NA	NA	0.0	0.0335320265405	NA	0.0	NA	NA	0.12361132429	0.0692121040509	NA	0.0	NA	0.260064432493	NA	0.0959604666378	NA	NA	0.0	0.0904897461535	NA	0.096024873638	0.551806072603	NA	0.0	NA	0.0	NA	0.282845890039	NA	NA	NA	NA	0.0	0.0	NA	0.0	0.206168383343	NA	NA	0.0337910137675	0.237818480755	0.0	NA	NA	0.0	0.0	0.0	NA	NA	NA	NA	NA	0.177374574	0.0	0.0	0.100596272282	0.340124774949	0.336749926715	0.0	NA	0.0	0.0	0.0	NA	NA	0.0	NA	0.0	NA	0.0	0.0	NA	0.0	0.0	0.0	NA	0.0	NA	NA	NA	0.0	0.0	NA	NA	0.0	NA	0.0	0.0	NA	NA	NA	NA	0.226897983481	0.0	NA	NA	NA	NA	NA	0.0	NA	NA	0.0734972121117	NA	0.0	NA	0.572649935308	NA	NA	0.383893601435	NA	0.0628733418693	0.296329616229	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	0.255561953725	NA	0.0	0.157858376637	NA	0.393736372309	0.0	0.119742668772	NA	0.393736372309	NA	1.01428769186	0.0	NA	NA	0.272044062708	NA	0.733760005611	NA	0.0660086032582	NA	0.900327296663	0.879392059123	NA	NA	0.0898683975317	0.0	0.0	0.0	NA	0.377579916714	1.12452142695	0.0	1.64185114287	0.029392400791	NA	NA	0.0	NA	0.490308287953	0.0	NA	NA	NA	0.0	NA	0.980828030569	NA	NA	0.746093235966	0.0	NA	NA	0.0	NA	0.54743287524	0.821826359884	NA	NA	0.720669950832	NA	NA	0.746435235532	0.0	0.0	0.852194994485	0.496018177117	NA	NA	NA	NA	NA	0.914227544844	0.0	NA	NA	0.0	NA	NA	NA	NA	0.0	0.0	0.0	0.0	NA	NA	0.0	NA	NA	0.0	0.0	NA	NA	0.0	NA	0.0	0.0	NA	NA
diff -r f4cc06e92530 -r a292aaf51735 predict/read_file.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/predict/read_file.py	Mon Sep 15 14:52:43 2014 -0400
@@ -0,0 +1,21 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import sys
+
+
+
+def read_t_file(in_file):
+    f = open(in_file);
+    result = [];
+    for aline in f.readlines():
+        temp = [];
+        tline = aline.strip();
+        tl = tline.split('\t');
+        for i in range(0, len(tl)):
+            temp.append(tl[i].strip());
+        result.append(temp);
+    f.close();
+    return result;
+
+
diff -r f4cc06e92530 -r a292aaf51735 predict/rtts_plot.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/predict/rtts_plot.py	Mon Sep 15 14:52:43 2014 -0400
@@ -0,0 +1,56 @@
+#!/usr/bin/env python
+#Make a plot of reactivity distribution
+
+import sys
+import numpy as np
+import matplotlib
+from pylab import *
+import math
+
+#Convert the reactivities (Make NA to 0)
+def convert_react(a):
+    r = []
+    for i in range(len(a)):
+        if a[i]!='NA':
+            r.append(float(a[i]))
+        else:
+            r.append(float(0))
+    return r
+        
+
+#Make a plot of the distribution
+def make_plot(ar,id_s,path):
+    N = len(ar)
+    a = convert_react(ar)
+    w = 1
+    ind = np.arange(N)
+
+    fig = figure()
+    fig, ax = subplots()
+    ax.bar(ind+w, a, width = w, color = 'r',edgecolor = 'r')
+    ax.set_ylabel('DMS Reactivity')
+    ax.set_xlabel('Nucleotide Index')
+
+    
+    mag = int(math.log(N,10))-1
+    tail = 10**mag
+
+    intervel = int(math.ceil(float(N)/tail)/5)
+    print(N)
+    print(intervel)
+    tl = []
+    k = 0
+    ax.set_xticks(np.arange(0,N,intervel*tail))
+    print(np.arange(0,N,intervel*tail))
+    ax.set_xticklabels(np.arange(0,N,intervel*tail))
+
+    ax.set_title(id_s+" reactivity distribution")
+    savefig(path+id_s+'.tif')
+
+
+
+    
+    
+    
+
+
diff -r f4cc06e92530 -r a292aaf51735 predict/tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/predict/tool_dependencies.xml	Mon Sep 15 14:52:43 2014 -0400
@@ -0,0 +1,9 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="biopython" version="1.61">
+        <repository changeset_revision="ae9dda584395" name="package_biopython_1_61" owner="biopython" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="numpy" version="1.7">
+        <repository changeset_revision="ef12a3a11d5b" name="package_numpy_1_7" owner="iuc" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>