# HG changeset patch
# User tyty
# Date 1410807321 14400
# Node ID b10c6790f01e9f891319a2c757b4fc32e1ed89c3
# Parent  1a909794e94d5d88163ce7fa6b807dee5d522a0b
Uploaded

diff -r 1a909794e94d -r b10c6790f01e get_reads/.DS_Store
Binary file get_reads/.DS_Store has changed
diff -r 1a909794e94d -r b10c6790f01e get_reads/get_read.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/get_reads/get_read.py	Mon Sep 15 14:55:21 2014 -0400
@@ -0,0 +1,77 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import sys
+#from galaxy.tools.read_file import *
+from Bio import SeqIO
+import os
+from read_file import *
+
+fasta_file = sys.argv[1]
+map_file = sys.argv[2]
+result_file = sys.argv[3]
+
+os.system("samtools view -F 0xfff "+map_file+"|cut -f 3,4 > map_info.txt") 
+
+fasta_sequences = SeqIO.parse(open(fasta_file),'fasta');
+length_seq = {};
+for seq in fasta_sequences:
+        nuc = seq.id;
+        length_seq[nuc] = len(seq.seq.tostring());
+
+
+
+mapping = {}
+transcripts = []
+
+f = open("map_info.txt");
+for aline in f.readlines():
+    tline = aline.strip();
+    tl = tline.split('\t');
+    if tl[0].strip() not in transcripts:
+        transcripts.append(tl[0].strip());
+        mapping[tl[0].strip()] = [];
+
+    mapping[tl[0].strip()].append(tl[1].strip());
+
+distribution = {};
+coverage = {};
+for transcript in length_seq:
+    distribution[transcript] = [];
+    for i in range(0, length_seq[transcript]):
+        distribution[transcript].append(0);
+    sum_count = float(0);
+    if transcript in mapping:
+        for j in range(0, len(mapping[transcript])):
+            index = mapping[transcript][j];
+            #count = reads[mapping[transcript][j][0]];
+            sum_count = sum_count + 1;
+            distribution[transcript][int(index)-1] = distribution[transcript][int(index)-1] + 1;
+            coverage[transcript] = float(sum_count)/float(length_seq[transcript]);
+    else:
+        coverage[transcript] = 0
+
+        
+        
+    
+
+h = file(result_file, 'w')
+for transcript in length_seq:
+    h.write(transcript);
+    h.write('\n')
+    for i in range(0, length_seq[transcript]):
+        h.write(str(distribution[transcript][i]))
+        h.write('\t')
+    h.write('\n')
+    h.write('\n')
+
+
+
+    
+
+f.close();
+h.close()
+
+
+
+
diff -r 1a909794e94d -r b10c6790f01e get_reads/get_read.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/get_reads/get_read.xml	Mon Sep 15 14:55:21 2014 -0400
@@ -0,0 +1,44 @@
+<tool id="get_read_pipeline" name="Get RT stop counts" version="1.0">
+	<description></description>
+	<command interpreter="python">get_read.py $lib_file $map_file $output </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>
+        </requirements>
+	<inputs>
+                <param name="lib_file" type="data" format="fasta" label="Library file (fasta)"/>
+		<param name="map_file" type="data" format="bam" label="Mapped file"/>
+	</inputs>
+	<outputs>
+		<data name="output" format="txt"/>
+	</outputs>
+        <tests>
+          <test>
+            <param name="lib_file" value="test.bam" />
+	    <param name="map_file" value="com_rna.txt" />
+	    <output name="output" file="get_RT_stop_test.out" />
+ 
+          </test>
+        </tests>
+
+	<help>
+
+
+**TIPS**:
+
+-----
+
+**Input**
+1. A mapped (bam) file from Bowtie (or any mapping program)
+2. Reference library sequences (fasta) used to map the reads
+
+-----
+
+**Output**:
+A text file with reverse transcription stop counts mapped to each nucleotide (RTSC file)	
+
+
+
+	</help>
+</tool>
diff -r 1a909794e94d -r b10c6790f01e get_reads/read_file.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/get_reads/read_file.py	Mon Sep 15 14:55:21 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 1a909794e94d -r b10c6790f01e get_reads/test.bam
Binary file get_reads/test.bam has changed
diff -r 1a909794e94d -r b10c6790f01e get_reads/tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/get_reads/tool_dependencies.xml	Mon Sep 15 14:55:21 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="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>
+</tool_dependency>
diff -r 1a909794e94d -r b10c6790f01e reactivity_cal/parse_dis_react.py
--- a/reactivity_cal/parse_dis_react.py	Mon Sep 15 14:54:59 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
-                
-                
-
-
-
-
-
-
-
-        
-
-
-
-
-
diff -r 1a909794e94d -r b10c6790f01e reactivity_cal/react_cal.py
--- a/reactivity_cal/react_cal.py	Mon Sep 15 14:54:59 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,151 +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]
-nt_spec = sys.argv[4]
-flag_in = sys.argv[5]
-threshold = sys.argv[6]
-output_file = sys.argv[7]
-
-
-distri_p = parse_dist(dist_file1)
-distri_m = parse_dist(dist_file2)
-threshold = float(threshold)
-
-print(flag_in)
-
-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')
-    if (trans[i].find('AT1G29930')==-1) and (trans[i].find('At1g29930')==-1):        
-        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))
-    else:
-        for j in range(len(distri_p[trans[i]])):
-            distri_p[trans[i]][j] = int(distri_p[trans[i]][j])
-        for j in range(len(distri_m[trans[i]])):
-            distri_m[trans[i]][j] = int(distri_m[trans[i]][j])       
-        s_p = sum(distri_p[trans[i]])
-        s_m = sum(distri_m[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)
-                f_m = float(distri_m[trans[i]][j])/float(s_m)
-                r.append((max(0,(f_p-f_m)))*100)
-                
-    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")
-    
-     
-            
-    
-    
-        
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-        
-
-
-
-
-
diff -r 1a909794e94d -r b10c6790f01e reactivity_cal/react_norm_function.py
--- a/reactivity_cal/react_norm_function.py	Mon Sep 15 14:54:59 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,114 +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]))
-#                    except:
-#                        print(react[t][i])
-#                        print(t)
-#                        print(i)
-
-    all_react.sort(reverse = True)
-    #print((all_react))
-    #print(all_react[int(len(all_react)*0.02)])
-    #print(all_react[int(len(all_react)*0.03)])
-    #print(all_react[int(len(all_react)*0.025)])
-    #print(all_react[int(len(all_react)*0.04)])
-    #print(all_react[int(len(all_react)*0.05)])
-    '''
-    mean = sum(all_react)/len(all_react)
-    print(mean)
-    temp = 0
-
-    for i in range(len(all_react)):
-        temp = temp+all_react[i]*all_react[i]
-    temp = temp/len(all_react)
-    sd = math.sqrt(temp-mean*mean)
-    '''
-    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':
-            if (t.find('AT1G29930')==-1) and (t.find('At1g29930')==-1):
-                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')
-            else:
-                for i in range((len(react[t])-1)):
-                    if react[t][i]!='NA':
-                        h.write(str(float(react[t][i])*2.6))
-                    else:
-                        h.write('NA')
-                    h.write('\t')
-                if react[t][i+1]!='NA':
-                    h.write(str(float(react[t][i])*2.6))
-                else:
-                    h.write('NA')
-                h.write('\n')
-                
-                
-
-    h.close()
-        
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-        
-
-
-
-
-
diff -r 1a909794e94d -r b10c6790f01e reactivity_cal/reactivity_calculation.xml
--- a/reactivity_cal/reactivity_calculation.xml	Mon Sep 15 14:54:59 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,48 +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>
-
-	<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>
diff -r 1a909794e94d -r b10c6790f01e reactivity_cal/read_file.py
--- a/reactivity_cal/read_file.py	Mon Sep 15 14:54:59 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 1a909794e94d -r b10c6790f01e reactivity_cal/separate_rna.py
--- a/reactivity_cal/separate_rna.py	Mon Sep 15 14:54:59 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,42 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-import sys
-from parse_dis_pac import *
-
-
-dist_file = sys.argv[1]
-cdna_file = sys.argv[2]
-rrna_file = sys.argv[3]
-
-dist = parse_dist(dist_file)
-dist = dist[1]
-hc = file(cdna_file, 'w')
-hr = file(rrna_file, 'w')
-
-for t in dist:
-    if t.find('AT') != -1:
-        hc.write(t)
-        hc.write('\n')
-        for i in range(len(dist[t])-1):
-            hc.write(dist[t][i])
-            hc.write('\t')
-        i = i+1
-        hc.write(dist[t][i])
-        hc.write('\n')
-    else:
-        hr.write(t)
-        hr.write('\n')
-        for i in range(len(dist[t])-1):
-            hr.write(dist[t][i])
-            hr.write('\t')
-        i = i+1
-        hr.write(dist[t][i])
-        hr.write('\n')
-
-hc.close()
-hr.close()
-
-    
-        
-
diff -r 1a909794e94d -r b10c6790f01e reactivity_cal/tool_dependencies.xml
--- a/reactivity_cal/tool_dependencies.xml	Mon Sep 15 14:54:59 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>