Binary file predict/.DS_Store has changed

Binary file predict/._predict_RNAs.xml has changed

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/predict/parse_dis_pac.py	Tue Dec 09 03:06:18 2014 -0500
@@ -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	Tue Dec 09 03:06:18 2014 -0500
@@ -0,0 +1,102 @@
+#RNA structure prediction & Output and illustrate reactivities
+
+import sys
+import shlex
+import subprocess
+import tarfile
+from parse_dis_pac import *
+from read_file import *
+from Bio import SeqIO
+import os
+from rtts_plot import *
+import random
+import string
+
+
+id_file = sys.argv[1]
+seq_file = sys.argv[2]
+predict_type = sys.argv[3]
+temperature = sys.argv[4]
+output_file = sys.argv[5]
+
+
+flag = False
+if predict_type!='silico': #input reactivity file if provided
+    react_file = sys.argv[6]
+    slope = sys.argv[7]
+    intercept = sys.argv[8]
+    react = parse_dist(react_file)
+    react = react[1]
+    flag = True
+
+syspath = os.getcwd()
+
+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)>100: #setup a limit of the number of sequence to be predicted
+    print("Number of sequences exceeds limitation!")
+    sys.exit(0)
+    
+
+#predict RNA structures
+output_directory = os.path.join(syspath, "output_files")
+if not os.path.exists(output_directory):
+    os.makedirs(output_directory)
+for i in range(len(ids)):
+    flag2 = 0
+    id_s = ids[i][0]
+    #print(id_s)
+    #Put RNA sequence and reactivities into files
+    if id_s in seqs:
+        fh = file(os.path.join(syspath,"temp.txt"), 'w')        
+        fh.write('>'+id_s)
+        fh.write('\n')
+        fh.write(seqs[id_s])
+        fh.close()
+        if not flag:
+            command = shlex.split('Fold %s -T %s %s' % (os.path.join(syspath, 'temp.txt'), temperature, os.path.join(output_directory, '%s.ct' % id_s)))
+            subprocess.call(command)
+        else:
+            if id_s in react:
+                fh = file(os.path.join(syspath, "constraint.txt"), 'w')
+                make_plot(react[id_s], id_s, output_directory) #make a plot of the distribution of the reactivites of the input RNA
+                for j in range(0, (len(react[id_s]))):
+                    if react[id_s][j]!='NA':
+                        fh.write(str(j+1))
+                        fh.write('\t')
+                        fh.write(str(react[id_s][j]))
+                        fh.write('\n')
+                    #h.write(str(react[id_s][j])) #Output the reactivities
+                    #h.write('\t')
+                fh.close()
+                #h.write('\n')
+                #h.write('\n')
+                command = shlex.split("Fold %s -sh %s -si %s -sm %s -T %s %s" % (os.path.join(syspath, "temp.txt"), 
+                                                             os.path.join(syspath, "constraint.txt"), intercept, slope, temperature, 
+                                                             os.path.join(output_directory, "%s.ct" % id_s)))
+                subprocess.call(command)
+            else:
+                print(id_s+" not in the data of react!")
+                flag2 = 1
+        if flag2 == 0:
+            command = shlex.split('draw %s.ct %s.ps' % (os.path.join(output_directory, id_s), os.path.join(output_directory, id_s)))
+            subprocess.call(command)
+    else:
+        print(id_s+" not in the data of sequences!")
+
+#Remove the unnecessary files
+tarball = tarfile.open(output_file, 'w:')
+for filename in os.listdir(output_directory):
+    filepath = os.path.join(output_directory, filename)
+    print filepath
+    tarball.add(filepath, arcname=filename)
+#print os.listdir(syspath)
+#print os.listdir(output_directory)
+# tarball.add('%s.tif' % os.path.join(syspath, id_s), arcname='%s.tif' % id_s)
+tarball.close()

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/predict/predict_RNAs.xml	Tue Dec 09 03:06:18 2014 -0500
@@ -0,0 +1,79 @@
+<tool id="predict_pipeline" name="RNA Structure Prediction" version="1.0">
+	<description></description>
+	<command interpreter="python">
+        #if $reactivity.type == "restraint"
+            predict_RNAs.py $rna_list $reference_file $reactivity.type $temperature $output $reactivity.reactivity_file $reactivity.slope $reactivity.intercept
+        #else
+            predict_RNAs.py $rna_list $reference_file $reactivity.type $temperature $output
+        #end if
+    </command>
+        <requirements>
+                <requirement type="package" version="1.61">biopython</requirement>
+                <requirement type="package" version="1.7.1">numpy</requirement>
+                <requirement type="package" version="1.2.1">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="temperature" type="float" value="310.15" label="Temperature (K)"/>
+        <conditional name="reactivity">
+            <param name="type" type="select" label="RNA structure prediction type">
+                <option value="silico">In silico</option>
+                <option value="restraint">With experimental restraints</option>
+            </param>
+            <when value="silico"/>
+            <when value="restraint">
+                <param name="reactivity_file" type="data" label="Reactivity file"/>
+                <param name="slope" type="float" value="1.8" label="Slope used with structural restraints"/>
+                <param name="intercept" type="float" value="-0.6" label="Intercept used with structural restraints"/>
+            </when>
+        </conditional>
+	
+	</inputs>
+	<outputs>
+		<data name="output" format=".tgz"/>
+	</outputs>
+
+	<help>
+
+
+**TIPS**:
+
+-----
+
+**Input**:
+
+* 1. A file with transcript Ids (Max num. 100), (each ID one line)
+* 2. Reference file (fasta) used to map the reads to
+* 3. Temperature for RNA structure prediction
+* [Optional]:
+* 1. A reactivity file with structural reactivity for each nucleotide on the sequence provided
+* 2. Slope used with structural restraints (default 1.8)
+* 3. Intercept used with structural restraints (default -0.6)
+
+-----
+
+**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]
+
+-----
+
+**Attention**
+
+Make sure any of the transcript Ids does not contain "|" or space!
+
+-----
+
+**Backend program**:
+
+* 1. This module is using RNAstructure (http://rna.urmc.rochester.edu/RNAstructure.html) as the backend program to predict RNA structures.
+* 2. Default parameters are used for RNAstructure expect -T (Temperature), -sm (slope used with SHAPE restraints) and -si (intercept used with SHAPE restraints) which users can specify the value
+
+
+
+	</help>
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/predict/rRNA.txt	Tue Dec 09 03:06:18 2014 -0500
@@ -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	Tue Dec 09 03:06:18 2014 -0500
@@ -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	Tue Dec 09 03:06:18 2014 -0500
@@ -0,0 +1,60 @@
+#!/usr/bin/env python
+#Make a plot of reactivity distribution
+
+import sys
+import os
+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):
+    font = {'family' : 'normal',
+            'weight' : 'bold',
+            'size'   : 16}
+    matplotlib.rc('font', **font)
+    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 = 'black',edgecolor = 'black')
+    ax.set_ylabel('Final Structural Reactivity (FSR)')
+    ax.set_xlabel('Nucleotide Number')
+
+    
+    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
+    upmax = int(math.ceil(float(N)/intervel/tail)*intervel*tail)+1
+    ax.set_xticks(np.arange(0,upmax,intervel*tail))
+    print(np.arange(0,upmax,intervel*tail))
+    ax.set_xticklabels(np.arange(0,upmax,intervel*tail))
+    savefig(os.path.join(path, id_s+'.tif'))
+
+
+
+    
+    
+    
+
+

Binary file predict/rtts_plot.pyc has changed