Mercurial > repos > johnheap > vapper
annotate Vap.py @ 5:7f3cfd8d114c draft
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author | johnheap |
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date | Mon, 03 Jun 2019 14:04:16 -0400 |
parents | 36cb22bd911d |
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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 argparse |
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32 #Entry .sort out the arguments |
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33 |
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34 pdfExport = False |
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35 #parser = argparse.ArgumentParser(description='Variant Antigen Profiler - the VAP.') |
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36 #parser.add_argument('name') |
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37 #parser.add_argument('-t','-T', action = 'store_true', default = False, help = "Transciptomic Pathway") |
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38 #parser.add_argument('-p','-P', action = 'store_true', default = False, help = "Export PDFs to HTML directory") |
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39 #parser.add_argument('strain') |
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40 #parser.add_argument('Forward_Read_File') |
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41 #parser.add_argument('Reverse_Read_File') |
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42 #parser.add_argument('htmlfile') |
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43 #parser.add_argument('htmlresource') |
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44 #parser.add_argument('heatmapFile') |
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45 #parser.add_argument('PCAFile') |
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46 #parser.add_argument('devheatmapFile') |
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47 #args = parser.parse_args() |
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48 |
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49 #we have numerous parameters.... |
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50 #hard code it for differnt types? |
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51 |
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52 |
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53 arguments = sys.argv |
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54 htmldir = arguments[len(arguments)-1] #last argument is always html_resource |
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55 if not os.path.exists(htmldir): |
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56 os.mkdir(htmldir) |
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57 |
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58 if arguments[1] == 'g_assemble': |
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59 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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60 Tryp_G.assemble(arguments,argdict) |
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61 if arguments[1] == 'g_contigs': |
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62 argdict = {'name':2, 'pdfexport':3, 'contigs':4, 'html_file':5, 'html_resource':6} |
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63 Tryp_G.contigs(arguments,argdict) |
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64 if arguments[1] == 'transcipt': |
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65 argdict = {'name':2, 'pdfexport': 3, 'strain': 4, 'forward': 5, 'reverse': 6, 'html_file': 7, 'html_resource': 8} |
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66 Tryp_T.transcriptomicProcess(arguments,argdict) |
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67 if arguments[1] == 'v_assemble': |
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68 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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69 Tryp_V.vivax_assemble(arguments,argdict) |
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70 if arguments[1] == 'v_contigs': |
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71 argdict = {'name':2, 'pdfexport':3, 'contigs':4, 'html_file':5, 'html_resource':6} |
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72 Tryp_V.vivax_contigs(arguments,argdict) |
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73 |
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74 |
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75 sys.exit() |
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76 |
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77 |
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78 |
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79 #if not os.path.exists(args.htmlresource): |
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80 # os.mkdir(args.htmlresource) |
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81 #if args.p: |
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82 # pdfExport = True |
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83 #if args.t: |
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84 # print ("Transcriptomic Pathway") |
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85 # Tryp_T.transcriptomicProcess(args.name, pdfExport, args.strain, args.Forward_Read_File, args.Reverse_Read_File, args.htmlfile, args.htmlresource) |
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86 #else: |
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87 #print ('Genomic Pathway') |
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88 #Tryp_G.test_output(args.name, args.htmlfile, args.htmlresource, args.heatmapFile, args.PCAFile,args.devheatmapFile) |
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89 # Tryp_G.genomicProcess(args.name, pdfExport, args.Forward_Read_File, args.Reverse_Read_File, args.htmlfile, args.htmlresource) |
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90 |
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91 |