changeset 116:62e8f7adf1ab draft

Uploaded

Binary file reactivity_cal/._.DS_Store has changed

Binary file reactivity_cal/._parse_dis_react.py has changed

Binary file reactivity_cal/._parse_dis_react.pyc has changed

Binary file reactivity_cal/._react_cal.py has changed

Binary file reactivity_cal/._react_norm_function.py has changed

Binary file reactivity_cal/._react_norm_function.pyc has changed

Binary file reactivity_cal/._reactivity_calculation.xml has changed

Binary file reactivity_cal/._read_file.py has changed

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/reactivity_cal/parse_dis_react.py	Tue Apr 14 14:16:55 2015 -0400
@@ -0,0 +1,51 @@
+#!/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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/reactivity_cal/react_cal.py	Tue Apr 14 14:16:55 2015 -0400
@@ -0,0 +1,135 @@
+#!/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
+import random
+import string
+
+
+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)
+
+
+syspathrs = os.getcwd()
+
+h = file(syspathrs+"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(float('%.3f'%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(float('%.3f'%r[k])))
+            h.write('\n')
+        else:
+            h.write('NA')
+            h.write('\n')
+            
+
+h.close()
+
+if flag_in:
+    react_norm((syspathrs+"react.txt"),output_file, threshold)
+else:
+    h_o = file(output_file, 'w')
+    f_i = open(syspathrs+"react.txt")
+    for aline in f_i.readlines():
+        h_o.write(aline.strip())
+        h_o.write('\n')
+os.system("rm -f "+syspathrs+"react.txt")
+
+#os.system("rm -r "+syspathrs)
+    
+     
+            
+    
+    
+        
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+        
+
+
+
+
+

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/reactivity_cal/react_norm_function.py	Tue Apr 14 14:16:55 2015 -0400
@@ -0,0 +1,82 @@
+#!/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(float('%.3f'%cap((float(react[t][i])/meight),capped))))
+                else:
+                    h.write('NA')
+                h.write('\t')
+            if react[t][i+1]!='NA':
+                h.write(str(float('%.3f'%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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/reactivity_cal/reactivity_calculation.xml	Tue Apr 14 14:16:55 2015 -0400
@@ -0,0 +1,62 @@
+<tool id="react_cal_pipeline" name="Reactivity Calculation" version="1.0">
+	<description>calculates structural reactivity on each nucleotide based on RT stop counts from the Get RT Stop Counts module</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="1.7.1">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 genome/transcriptome"/>
+                <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="Threshold 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>
+
+
+**Function**
+
+* Reactivity Calculation calculates the structural reactivity on each nucleotide based on an RT stop count file containing the RT stop count on each nucleotide, typically the output from the Get RT Stop Counts module.
+
+-----
+
+**Input**:
+
+* 1. RTSC files (Output of Get RT Stop Counts) for (+) and (-) library
+* 2. Reference file (fasta) used to map the reads to
+* 3. Nucleotide Specificity (Type of nucleotides 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>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/reactivity_cal/read_file.py	Tue Apr 14 14:16:55 2015 -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;
+
+