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comparison Vap.py @ 0:36cb22bd911d draft

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planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
author johnheap
date Wed, 04 Jul 2018 16:39:13 -0400
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children c4463e84a7ea
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-1:000000000000 0:36cb22bd911d
1 """
2 * Copyright 2018 University of Liverpool
3 * Author: John Heap, Computational Biology Facility, UoL
4 * Based on original scripts of Sara Silva Pereira, Institute of Infection and Global Health, UoL
5 *
6 * Licensed under the Apache License, Version 2.0 (the "License");
7 * you may not use this file except in compliance with the License.
8 * You may obtain a copy of the License at
9 *
10 * http://www.apache.org/licenses/LICENSE-2.0
11 *
12 * Unless required by applicable law or agreed to in writing, software
13 * distributed under the License is distributed on an "AS IS" BASIS,
14 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
15 * See the License for the specific language governing permissions and
16 * limitations under the License.
17 *
18 """
19 #import subprocess
20 #import re
21 import os
22 import sys
23 #import pandas as pd
24 #import numpy as np
25 #import seaborn as sns
26 #import matplotlib.pyplot as plt
27 #from matplotlib.mlab import PCA
28 import Tryp_G
29 import Tryp_T
30 import Tryp_V
31 import argparse
32 #Entry .sort out the arguments
33
34 pdfExport = False
35 #parser = argparse.ArgumentParser(description='Variant Antigen Profiler - the VAP.')
36 #parser.add_argument('name')
37 #parser.add_argument('-t','-T', action = 'store_true', default = False, help = "Transciptomic Pathway")
38 #parser.add_argument('-p','-P', action = 'store_true', default = False, help = "Export PDFs to HTML directory")
39 #parser.add_argument('strain')
40 #parser.add_argument('Forward_Read_File')
41 #parser.add_argument('Reverse_Read_File')
42 #parser.add_argument('htmlfile')
43 #parser.add_argument('htmlresource')
44 #parser.add_argument('heatmapFile')
45 #parser.add_argument('PCAFile')
46 #parser.add_argument('devheatmapFile')
47 #args = parser.parse_args()
48
49 #we have numerous parameters....
50 #hard code it for differnt types?
51
52
53 arguments = sys.argv
54 htmldir = arguments[len(arguments)-1] #last argument is always html_resource
55 if not os.path.exists(htmldir):
56 os.mkdir(htmldir)
57
58 if arguments[1] == 'g_assemble':
59 argdict = {'name':2, 'pdfexport':3, 'kmers':4,'inslen':5, 'covcut':6, 'forward':7, 'reverse':8, 'html_file':9, 'html_resource':10}
60 Tryp_G.assemble(arguments,argdict)
61 if arguments[1] == 'g_contigs':
62 argdict = {'name':2, 'pdfexport':3, 'contigs':4, 'html_file':5, 'html_resource':6}
63 Tryp_G.contigs(arguments,argdict)
64 if arguments[1] == 'transcipt':
65 argdict = {'name':2, 'pdfexport': 3, 'strain': 4, 'forward': 5, 'reverse': 6, 'html_file': 7, 'html_resource': 8}
66 Tryp_T.transcriptomicProcess(arguments,argdict)
67 if arguments[1] == 'v_assemble':
68 argdict = {'name':2, 'pdfexport':3, 'kmers':4,'inslen':5, 'covcut':6, 'forward':7, 'reverse':8, 'html_file':9, 'html_resource':10}
69 Tryp_V.vivax_assemble(arguments,argdict)
70 if arguments[1] == 'v_contigs':
71 argdict = {'name':2, 'pdfexport':3, 'contigs':4, 'html_file':5, 'html_resource':6}
72 Tryp_V.vivax_contigs(arguments,argdict)
73
74
75 sys.exit()
76
77
78
79 #if not os.path.exists(args.htmlresource):
80 # os.mkdir(args.htmlresource)
81 #if args.p:
82 # pdfExport = True
83 #if args.t:
84 # print ("Transcriptomic Pathway")
85 # Tryp_T.transcriptomicProcess(args.name, pdfExport, args.strain, args.Forward_Read_File, args.Reverse_Read_File, args.htmlfile, args.htmlresource)
86 #else:
87 #print ('Genomic Pathway')
88 #Tryp_G.test_output(args.name, args.htmlfile, args.htmlresource, args.heatmapFile, args.PCAFile,args.devheatmapFile)
89 # Tryp_G.genomicProcess(args.name, pdfExport, args.Forward_Read_File, args.Reverse_Read_File, args.htmlfile, args.htmlresource)
90
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