Mercurial > repos > tyty > structurefold

changeset 27:564795252d1a draft

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Uploaded
author tyty
date Mon, 20 Oct 2014 14:42:09 -0400
parents 8bf6c855353b
children cfb6e6e68917
files predict/.DS_Store predict/._.DS_Store predict/._tool_dependencies.xml predict/parse_dis_pac.py predict/parse_dis_pac.pyc predict/predict_RNAs.py predict/predict_RNAs.xml predict/predict_RNAs.xml~ predict/rRNA.txt predict/read_file.py predict/read_file.pyc predict/rtts_plot.py predict/rtts_plot.pyc predict/tool_dependencies.xml predict/tool_dependencies.xml~ reactivity_cal/._.DS_Store reactivity_cal/._tool_dependencies.xml reactivity_cal/dis_f_N1Am_rrna.txt reactivity_cal/dis_f_N1Ap_rrna.txt reactivity_cal/parse_dis_react.py reactivity_cal/parse_dis_react.pyc reactivity_cal/rRNA.txt reactivity_cal/react_cal.py reactivity_cal/react_norm_function.py reactivity_cal/react_norm_function.pyc reactivity_cal/reactivity_calculation.xml reactivity_cal/reactivity_calculation.xml~ reactivity_cal/read_file.py reactivity_cal/tool_dependencies.xml
diffstat 29 files changed, 364 insertions(+), 435 deletions(-) [+]
line wrap: on
line diff
Binary file predict/.DS_Store has changed
Binary file predict/._.DS_Store has changed
Binary file predict/._tool_dependencies.xml has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/predict/parse_dis_pac.py	Mon Oct 20 14:42:09 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
+                
+                
+
+
+
+
+
+
+
+        
+
+
+
+
+
Binary file predict/parse_dis_pac.pyc has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/predict/predict_RNAs.py	Mon Oct 20 14:42:09 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/"+"*.* 2>"+syspath+"log.txt")
+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()
+    
+    
+
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/predict/predict_RNAs.xml	Mon Oct 20 14:42:09 2014 -0400
@@ -0,0 +1,59 @@
+<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>
+                <requirement type="package" version="1.2">matplotlib</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"/>
+	
+	</inputs>
+	<outputs>
+		<data name="output" format=".tgz"/>
+	</outputs>
+    <tests>
+        <test>
+            <param name="rna_list" value="id_list_test.txt" />
+	        <param name="reference_file" value="cdna.txt" />
+            <param name="reactivity_file" value="mRNA_react_test2.txt" />
+	        <output name="output" file="structures.out" />
+        </test>
+    </tests>
+	<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>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/predict/predict_RNAs.xml~	Mon Oct 20 14:42:09 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>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/predict/rRNA.txt	Mon Oct 20 14:42:09 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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/predict/read_file.py	Mon Oct 20 14:42:09 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;
+
+
Binary file predict/read_file.pyc has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/predict/rtts_plot.py	Mon Oct 20 14:42:09 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')
+
+
+
+    
+    
+    
+
+
Binary file predict/rtts_plot.pyc has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/predict/tool_dependencies.xml	Mon Oct 20 14:42:09 2014 -0400
@@ -0,0 +1,12 @@
+<?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="matplotlib" version="1.2">
+        <repository changeset_revision="fe60617380df" name="package_matplotlib_1_2" owner="iuc" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/predict/tool_dependencies.xml~	Mon Oct 20 14:42:09 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>
Binary file reactivity_cal/._.DS_Store has changed
Binary file reactivity_cal/._tool_dependencies.xml has changed
--- a/reactivity_cal/dis_f_N1Am_rrna.txt	Mon Oct 20 14:41:56 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,12 +0,0 @@
-gi|186498419|ref|NR_022453.1|
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-coverage:3967.112
-Arabidopsis
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--- a/reactivity_cal/dis_f_N1Ap_rrna.txt	Mon Oct 20 14:41:56 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,12 +0,0 @@
-gi|186498419|ref|NR_022453.1|
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-coverage:6327.99377778
-Arabidopsis
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-coverage:43.1900826446
-gi|20197903:2706-4513
-918451	43069	4973	6069	5424	764	1308	1439	883	907	987	3034	389	406	952	935	228	1164	4117	891	3486	1385	2729	4818	1258	26713	4029	5575	4375	1242	1070	2107	920	1244	1091	1165	4373	1897	5508	17168	30987	6744	39793	35181	2869	4645	4692	3044	1437	1272	3410	3227	3218	950	11595	1582	3975	4126	3534	2904	9622	9201	2662	5093	17776	53180	1503	5034	36896	3073	2696	12752	92843	89306	51420	20625	12112	19628	14536	7588	16552	7625	2887	5143	2395	77142	8914	1213	1504	2871	807	9425	1820	12549	1146	1756	873	702	4748	1983	28475	12593	4907	15539	18662	26723	5381	1232	6179	7188	7257	11050	8482	3815	5990	5082	1806	1922	2605	1940	1266	5733	1528	1833	4406	5121	2372	5536	3055	7605	63077	12644	78932	88354	15542	70445	7243	6242	120346	2540	1657	3245	25109	5755	1160	8889	5851	2503	876	7493	5714	9802	13634	8462	14457	8287	7986	2320	4129	8613	1888	5304	4607	2516	6019	15661	9337	2463	7209	1824	3285	2368	4304	947	36403	95330	40526	20022	54545	77764	3922	2515	3015	414	1370	14283	58088	11847	6695	24021	59631	6958	3539	4469	16242	340311	7244	1837	18429	8372	18021	5639	41746	21583	14255	9732	18318	11221	6535	10615	10301	40428	533599	326270	55341	36178	28527	8780	4316	27359	1402	2267	21704	3585	2449	2389	1205	6044	1632	2498	21387	25280	15320	4162	1764	3727	2635	19546	22097	8739	4664	21700	11278	21131	48044	2632	42293	5936	3669	21387	10312	18637	1858	25311	159741	5693	23447	3845	15343	7781	1209	18376	1883	2889	15421	5395	5221	589	16571	255673	5036	4649	4379	14806	6242	1153	6334	1207	2127	15500	269146	206619	25198	83043	13150	15591	7979	9163	13341	1153	2181	21654	3397	11882	2120	25839	34277	8235	17713	14707	33769	34611	23409	16045	46807	10245	7192	5440	2570	1530	629	5093	2209	1933	4632	13485	118398	3529	13894	12849	5579	3313	3197	12455	2575	1353	4839	1286	818	418	463	855	938	549	6614	4199	3176	3182	462	311	873	513	175	195	2569	689	217	3286	1004	486	365	683	978	2539	987	1931	14123	358	1065	201	1443	638	861	7076	735	494	607	1394	4512	5974	12877	3584	1718	2029	6966	1725	717	1255	2196	587	1166	3496	589	737	859	614	434	174	582	691	588	2404	1393	481	165	413	280	186	191	350	783	1657	971	1473	6521	258	1769	575	323	224	1775	321	167	3255	221	2023	11024	1286	569	4550	17400	11662	718	1234	4560	3160	642	257	2328	529	894	1211	579	256	506	909	688	2805	882	12678	27229	9905	8194	690	1257	786	734	852	2316	1227	1305	203	1235	585	1289	6637	6275	7344	596	2993	1093	199	81	784	866	959	1940	527	2090	452	362	7523	6256	18337	9647	5141	8828	3798	17697	2009	2458	9177	2905	5062	4758	1977	2374	922	306	215	1332	239	332	783	875	5373	16505	153966	10369	17786	5145	3987	2840	388	2542	1062	2393	3988	10780	46495	35443	5441	2750	3089	7490	44543	4522	7389	30017	41341	6083	16256	11272	14499	17752	12640	4905	12457	10533	8046	11038	3131	1047	9235	2518	7924	2114	8155	786504	20595	4724	18877	16816	3257	20972	174536	10915	10591	53044	9521	3903	5021	2460	3040	4609	4420	5187	966	207182	10038	4869	7684	1525	3982	2569	2485	342	1094	2782	1929	8190	6125	3783	3835	3938	1472	2345	1122	3299	13563	7847	15191	53606	151932	10494	12925	6127	1369	14734	2286	1409	4612	2395	20399	21833	37032	17626	2744	15445	6995	5652	15687	23622	24690	300234	38628	20789	7096	26987	63959	6745	13800	4071	5326	10434	3218	2338	5241	24342	17104	31725	24079	54301	80045	16097	14430	19838	3836	1915	20476	5640	2057	19218	17512	9583	19429	14930	4053	2368	36692	28478	17960	12763	3211	15723	17455	4262	15836	5574	17075	2971	1549	11262	1816	2481	3031	1711	2245	3302	2239	5581	5436	898	3189	6402	7369	19431	10181	13982	19518	19378	6052	3397	7060	48792	49466	166394	16294	11481	7588	2631	9634	818	7222	8071	5098	50033	3363	2907	3316	2831	28201	23752	15257	6539	31273	20417	8330	18882	2784	7312	11264	5719	37305	11156	34369	28532	7521	2088	5106	136216	6760	3184	8826	4505	17420	89725	5786	9835	47563	42284	228449	23151	10905	9629	2291	852	539	21600	1595	1643	83308	3168	9230	1691	5252	3309	1515	5225	4626	1267	7645	10913	3289	11718	160149	96128	20051	4231	10627	21149	6156	9864	8341	10069	2123	20394	14350	9726	19497	27938	98863	14126	12365	11455	5934	8883	3699	2200	1856	2930	29028	20229	4265	13036	10997	123690	13292	23786	7293	26281	10459	4324	80443	74236	29597	4360	3106	7668	2936	50151	6032	8456	41215	30315	72582	22633	82098	56991	7444	11502	18815	3986	51306	4799	3007	3601	2699	32496	8227	8523	51338	3731	23833	383982	16734	54704	181869	15780	44891	8843	61934	8722	3511	9541	2014	2082	9791	12879	1256	1769	16492	23018	25711	3425	5757	7748	6637	8538	2421	1180	2306	3558	2511	6676	15736	2895	16995	12150	784	15694	19837	2235	2291	6787	14289	13577	33423	7455	104407	25193	11741	76444	149786	13133	19339	38730	9696	10093	11742	2843	2973	16682	8778	4261	3432	9341	2088	3519	5195	2142	3650	23502	21304	29334	11102	24475	3829	8448	25057	29207	4072	4295	15963	7557	13441	16457	6903	7517	18114	2888	15355	2912	9314	10223	7355	6996	23929	34758	32336	23582	18784	13062	4052	11500	5164	4390	4450	43219	15862	13078	12019	32352	11400	10789	7759	44295	10190	3755	43157	4945	3789	27000	728401	15353	25752	37886	6521	5833	10411	4997	13530	17532	19474	11376	13583	5615	59799	19137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-coverage:14437.7997788
--- a/reactivity_cal/parse_dis_react.py	Mon Oct 20 14:41:56 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,51 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-import sys
-
-def parse_dist(in_file):
-    result = []
-    distribution = {}
-    name = []
-    f = open(in_file)
-    flag = 0
-    for aline in f.readlines():
-        line = aline.strip()
-        dis = line.strip()
-        dist = dis.split('\t')
-        if len(dist) > 0:
-            if len(dist) == 1:
-                if dist[0].strip().find('coverage')==-1:
-                    if flag == 0:
-                        name.append(line)
-                        flag = 1
-                        t_name = line
-                    else:
-                        distribution[t_name] = 'null'
-                        name.append(line)
-                        flag = 1
-                        t_name = line
-            else:
-                distri = []
-                for i in range(0, len(dist)):
-                    distri.append(dist[i].strip())
-                distribution[t_name] = distri
-                flag = 0
-    result.append(name)
-    result.append(distribution)
-    f.close()
-    return result
-                
-                
-
-
-
-
-
-
-
-        
-
-
-
-
-
Binary file reactivity_cal/parse_dis_react.pyc has changed
--- a/reactivity_cal/rRNA.txt	Mon Oct 20 14:41:56 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
->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
--- a/reactivity_cal/react_cal.py	Mon Oct 20 14:41:56 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,136 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-import sys
-from Bio import SeqIO
-import math
-from parse_dis_react import *
-from react_norm_function import *
-import os
-
-
-dist_file1 = sys.argv[1] #plus library
-dist_file2 = sys.argv[2] #minus library
-seq_file = sys.argv[3] #Reference library(genome/cDNA)
-nt_spec = sys.argv[4] #only show reactivity for AC or ATCG
-flag_in = sys.argv[5] # perform 2-8% normalization (1) or not (0)
-threshold = sys.argv[6] #Threshold to cap the reactivities
-output_file = sys.argv[7]
-
-
-distri_p = parse_dist(dist_file1)
-distri_m = parse_dist(dist_file2)
-threshold = float(threshold)
-
-
-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+'/' 
-
-h = file(syspath+"react.txt",'w')
-flag_in = int(flag_in)
-
-seqs = SeqIO.parse(open(seq_file),'fasta');
-nt_s = set()
-for i in range(len(nt_spec)):
-    nt_s.add(nt_spec[i])
-
-flag = 0
-trans = []
-distri_p = distri_p[1]
-distri_m = distri_m[1]
-
-#thres = int(threshold)
-
-
-transcripts = {}
-for seq in seqs:
-    n = seq.id
-    trans.append(n)
-    transcripts[n] = seq.seq.tostring()
-    
-
-#print(distri_p)
-        
-
-for i in range(0, len(trans)):
-    h.write(trans[i])
-    h.write('\n')       
-    for j in range(len(distri_p[trans[i]])):
-        distri_p[trans[i]][j] = math.log((int(distri_p[trans[i]][j])+1),math.e)
-    for j in range(len(distri_m[trans[i]])):
-        distri_m[trans[i]][j] = math.log((int(distri_m[trans[i]][j])+1),math.e)       
-    s_p = sum(distri_p[trans[i]])
-    s_m = sum(distri_m[trans[i]])
-    length = len(distri_p[trans[i]])
-    if s_p!= 0 and s_m!= 0:
-        r = []
-        for j in range(0, len(distri_p[trans[i]])):
-            f_p = (float(distri_p[trans[i]][j]))/float(s_p)*length
-            f_m = (float(distri_m[trans[i]][j]))/float(s_m)*length
-            raw_react = f_p-f_m
-            r.append(max(0, raw_react))
-                
-    if s_p!= 0 and s_m!= 0:    
-        for k in range(1,(len(r)-1)):
-            if transcripts[trans[i]][k-1] in nt_s:
-                h.write(str(r[k]))
-                h.write('\t')
-            else:
-                h.write('NA')
-                h.write('\t')
-        k = k+1
-        if transcripts[trans[i]][k-1] in nt_s:
-            h.write(str(r[k]))
-            h.write('\n')
-        else:
-            h.write('NA')
-            h.write('\n')
-            
-
-h.close()
-
-if flag_in:
-    react_norm((syspath+"react.txt"),output_file, threshold)
-else:
-    h_o = file(output_file, 'w')
-    f_i = open(syspath+"react.txt")
-    for aline in f_i.readlines():
-        h_o.write(aline.strip())
-        h_o.write('\n')
-os.system("rm -f "+syspath+"react.txt")
-    
-     
-            
-    
-    
-        
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-        
-
-
-
-
-
--- a/reactivity_cal/react_norm_function.py	Mon Oct 20 14:41:56 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,82 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-import sys
-from Bio import SeqIO
-import math
-from parse_dis_react import *
-
-def cap(a,value):
-    if a>=value:
-        return value
-    else:
-        return a
-
-def react_norm(react_file, result_file, capped_value):
-    print("Normalizing.....")
-    react1 = parse_dist(react_file)
-    react = react1[1]
-    h = file(result_file, 'w')
-
-    capped = int(capped_value)
-
-    all_react = []
-
-
-    for t in react:
-        if react[t]!='null':
-            for i in range(len(react[t])):
-                if react[t][i]!='NA':                   
-                    all_react.append(float(react[t][i]))
-
-
-    all_react.sort(reverse = True)
-
-
-    eight = all_react[int(len(all_react)*0.02):int(len(all_react)*0.1)]
-    meight = sum(eight)/len(eight)
-
-    for t in react:
-        h.write(t)
-        h.write('\n')
-        if react[t]!='null':
-            for i in range((len(react[t])-1)):
-                if react[t][i]!='NA':
-                    h.write(str(cap((float(react[t][i])/meight),capped)))
-                else:
-                    h.write('NA')
-                h.write('\t')
-            if react[t][i+1]!='NA':
-                h.write(str(cap((float(react[t][i+1])/meight),capped)))
-            else:
-                h.write('NA')
-            h.write('\n')
-
-    h.close()
-        
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-        
-
-
-
-
-
Binary file reactivity_cal/react_norm_function.pyc has changed
--- a/reactivity_cal/reactivity_calculation.xml	Mon Oct 20 14:41:56 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,60 +0,0 @@
-<tool id="react_cal_pipeline" name="Reactivity calculation" version="1.0">
-	<description></description>
-	<command interpreter="python">react_cal.py $dist_file1 $dist_file2 $seq_file $nt_spec $flag_in $threshold $output </command>
-        <requirements>
-                <requirement type="package" version="1.61">biopython</requirement>
-                <requirement type="package" version="1.7">numpy</requirement>
-        </requirements>
-	<inputs>
-                <param name="dist_file1" type="data" format="txt" label="RTSC file for (+) library"/>
-		        <param name="dist_file2" type="data" format="txt" label="RTSC file for (-) library"/>
-                <param name="seq_file" type="data" format="fasta" label="Reference library"/>
-                <param name="nt_spec" type="select" label="Nucleotide specificity">
-                    <option value="AC">AC</option>
-                    <option value="ATCG">AUCG</option>
-                </param>
-                <param name="flag_in" type="boolean" checked="true" truevalue = "1" falsevalue = "0" label="Normalization is performed if checked"/>
-                <param name="threshold" type="float" value = "7" optional = "true" label="Value to cap the reactivities"/>
-	</inputs>
-	<outputs>
-		<data name="output" format="txt"/>
-	</outputs>
-    <tests>
-        <test>
-            <param name="dist_file1" value="dis_f_N1Ap_rrna.txt" />
-	        <param name="dist_file2" value="dis_f_N1Am_rrna.txt" />
-            <param name="seq_file" value="rRNA.txt" />
-            <param name="nt_spec" value="AC" />
-            <param name="flag_in" value="1" />
-            <param name="threshold" value="7" />
-	        <output name="output" file="DMS_reactivities.out" />
- 
-          </test>
-    </tests>
-
-	<help>
-
-
-**TIPS**:
-
------
-
-**Input**:
-
-* 1. RTSC files (Output of II) for (+) and (-) library
-* 2. Reference file (fasta) used to map the reads
-* 3. Nucleotide Specificity (Type of nucleotide to have reactivity, e.g. AC for DMS and ACTG for SHAPE)
-* [Optional]:
-* 1. A threshold to cap the structural reactivities. {Default: 7}
-* 2. Flag that determines whether to perform 2%-8% normalization {Default: yes}
-
------
-
-**Output**:
-
-A text file with structural reactivity for each nucleotide (Reactivity file)
-
-
-
-	</help>
-</tool>
--- a/reactivity_cal/reactivity_calculation.xml~	Mon Oct 20 14:41:56 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,44 +0,0 @@
-<tool id="react_cal_pipeline" name="Reactivity calculation" version="1.0">
-	<description></description>
-	<command interpreter="python">react_cal.py $dist_file1 $dist_file2 $seq_file $nt_spec $flag_in $threshold $output </command>
-        <requirements>
-                <requirement type="package" version="1.61">biopython</requirement>
-        </requirements>
-	<inputs>
-                <param name="dist_file1" type="data" format="txt" label="RTSC file for (+) library"/>
-		<param name="dist_file2" type="data" format="txt" label="RTSC file for (-) library"/>
-                <param name="seq_file" type="data" format="fasta" label="Reference library"/>
-                <param name="nt_spec" type="text" value = "AC" label="Nucleotide specificity"/>
-                <param name="flag_in" type="boolean" checked="true" truevalue = "1" falsevalue = "0" label="Normalization is performed if checked"/>
-                <param name="threshold" type="float" value = "7" label="Value to cap the reactivities"/>
-	</inputs>
-	<outputs>
-		<data name="output" format="txt"/>
-	</outputs>
-
-	<help>
-
-
-**TIPS**:
-
------
-
-**Input**:
-
-* 1. RTSC files (Output of II) for (+) and (-) library
-* 2. Reference file (fasta) used to map the reads
-* 3. Nucleotide Specificity (Type of nucleotide to have reactivity, e.g. AC for DMS and ACTG for SHAPE)
-* [Optional]:
-* 1. A threshold to cap the structural reactivities. {Default: 7}
-* 2. Flag that determines whether to perform 2%-8% normalization {Default: yes}
-
------
-
-**Output**:
-
-A text file with structural reactivity for each nucleotide (Reactivity file)
-
-
-
-	</help>
-</tool>
--- a/reactivity_cal/read_file.py	Mon Oct 20 14:41:56 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;
-
-
--- a/reactivity_cal/tool_dependencies.xml	Mon Oct 20 14:41:56 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,9 +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>
-</tool_dependency>