Mercurial > repos > tyty > structurefold

changeset 29:003096bd038c draft

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Deleted selected files
author tyty
date Mon, 20 Oct 2014 14:43:40 -0400
parents cfb6e6e68917
children 4d81d174dece
files Iterative_mapping/.DS_Store get_reads/.DS_Store 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~
diffstat 17 files changed, 0 insertions(+), 364 deletions(-) [+]
line wrap: on
line diff
Binary file Iterative_mapping/.DS_Store has changed
Binary file get_reads/.DS_Store has changed
Binary file predict/.DS_Store has changed
Binary file predict/._.DS_Store has changed
Binary file predict/._tool_dependencies.xml has changed
--- a/predict/parse_dis_pac.py	Mon Oct 20 14:42:42 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,43 +0,0 @@
-#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
--- a/predict/predict_RNAs.py	Mon Oct 20 14:42:42 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,93 +0,0 @@
-#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()
-    
-    
-
-
-
--- a/predict/predict_RNAs.xml	Mon Oct 20 14:42:42 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,59 +0,0 @@
-<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>
--- a/predict/predict_RNAs.xml~	Mon Oct 20 14:42:42 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,63 +0,0 @@
-<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>
--- a/predict/rRNA.txt	Mon Oct 20 14:42:42 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/predict/read_file.py	Mon Oct 20 14:42:42 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;
-
-
Binary file predict/read_file.pyc has changed
--- a/predict/rtts_plot.py	Mon Oct 20 14:42:42 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,56 +0,0 @@
-#!/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
--- a/predict/tool_dependencies.xml	Mon Oct 20 14:42:42 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,12 +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="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>
--- a/predict/tool_dependencies.xml~	Mon Oct 20 14:42:42 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>