20
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1 """
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2 * Copyright 2018 University of Liverpool
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3 * Author: John Heap, Computational Biology Facility, UoL
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4 * Based on original scripts of Sara Silva Pereira, Institute of Infection and Global Health, UoL
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5 *
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6 * Licensed under the Apache License, Version 2.0 (the "License");
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7 * you may not use this file except in compliance with the License.
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8 * You may obtain a copy of the License at
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9 *
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10 * http://www.apache.org/licenses/LICENSE-2.0
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11 *
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12 * Unless required by applicable law or agreed to in writing, software
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13 * distributed under the License is distributed on an "AS IS" BASIS,
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14 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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15 * See the License for the specific language governing permissions and
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16 * limitations under the License.
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17 *
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18 """
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19 #import subprocess
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20 #import re
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21 import os
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22 import sys
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23 #import pandas as pd
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24 #import numpy as np
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25 #import seaborn as sns
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26 #import matplotlib.pyplot as plt
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27 #from matplotlib.mlab import PCA
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28 import Tryp_G
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29 import Tryp_T
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30 import Tryp_V
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31 import Tryp_V_T
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32 import argparse
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33 #Entry .sort out the arguments
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34
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20
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35 pdfExport = False
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36 #parser = argparse.ArgumentParser(description='Variant Antigen Profiler - the VAP.')
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37 #parser.add_argument('name')
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38 #parser.add_argument('-t','-T', action = 'store_true', default = False, help = "Transciptomic Pathway")
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39 #parser.add_argument('-p','-P', action = 'store_true', default = False, help = "Export PDFs to HTML directory")
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40 #parser.add_argument('strain')
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41 #parser.add_argument('Forward_Read_File')
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42 #parser.add_argument('Reverse_Read_File')
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43 #parser.add_argument('htmlfile')
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44 #parser.add_argument('htmlresource')
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45 #parser.add_argument('heatmapFile')
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46 #parser.add_argument('PCAFile')
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47 #parser.add_argument('devheatmapFile')
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48 #args = parser.parse_args()
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49
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20
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50 #we have numerous parameters....
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51 #hard code it for differnt types?
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52
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53
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54 arguments = sys.argv
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55 htmldir = arguments[len(arguments)-1] #last argument is always html_resource
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56 if not os.path.exists(htmldir):
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57 os.mkdir(htmldir)
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58
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59 if arguments[1] == 'g_assemble':
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60 argdict = {'name':2, 'pdfexport':3, 'kmers':4,'inslen':5, 'covcut':6, 'forward':7, 'reverse':8, 'html_file':9, 'html_resource':10}
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61 Tryp_G.assemble(arguments,argdict)
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62 if arguments[1] == 'g_contigs':
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63 argdict = {'name':2, 'pdfexport':3, 'contigs':4, 'html_file':5, 'html_resource':6}
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64 Tryp_G.contigs(arguments,argdict)
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65 if arguments[1] == 'transcipt':
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66 argdict = {'name':2, 'pdfexport': 3, 'strain': 4, 'forward': 5, 'reverse': 6, 'html_file': 7, 'html_resource': 8}
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67 Tryp_T.transcriptomicProcess(arguments,argdict)
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68 if arguments[1] == 'v_assemble':
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69 argdict = {'name':2, 'pdfexport':3, 'kmers':4,'inslen':5, 'covcut':6, 'forward':7, 'reverse':8, 'html_file':9, 'html_resource':10}
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70 Tryp_V.vivax_assemble(arguments,argdict)
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71 if arguments[1] == 'v_contigs':
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72 argdict = {'name':2, 'pdfexport':3, 'contigs':4, 'html_file':5, 'html_resource':6}
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73 Tryp_V.vivax_contigs(arguments,argdict)
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74 if arguments[1] == 'v_transcript':
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75 argdict = {'name':2, 'pdfexport': 3, 'refFastq': 4, 'forward': 5, 'reverse': 6, 'html_file': 7, 'html_resource': 8}
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76 Tryp_V_T.transcriptomicProcess(arguments,argdict)
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77
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78
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79 sys.exit()
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80
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