| Previous changeset 10:6450a72e8f6b (2019-06-03) Next changeset 12:491102c84b20 (2019-06-03) |
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Vap.py |
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| diff -r 6450a72e8f6b -r c4463e84a7ea Vap.py --- a/Vap.py Mon Jun 03 14:11:12 2019 -0400 +++ b/Vap.py Mon Jun 03 14:12:06 2019 -0400 |
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| b'@@ -1,91 +1,1165 @@\n-"""\r\n- * Copyright 2018 University of Liverpool\r\n- * Author: John Heap, Computational Biology Facility, UoL\r\n- * Based on original scripts of Sara Silva Pereira, Institute of Infection and Global Health, UoL\r\n- *\r\n- * Licensed under the Apache License, Version 2.0 (the "License");\r\n- * you may not use this file except in compliance with the License.\r\n- * You may obtain a copy of the License at\r\n- *\r\n- * http://www.apache.org/licenses/LICENSE-2.0\r\n- *\r\n- * Unless required by applicable law or agreed to in writing, software\r\n- * distributed under the License is distributed on an "AS IS" BASIS,\r\n- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\r\n- * See the License for the specific language governing permissions and\r\n- * limitations under the License.\r\n- *\r\n- """\r\n-#import subprocess\r\n-#import re\r\n-import os\r\n-import sys\r\n-#import pandas as pd\r\n-#import numpy as np\r\n-#import seaborn as sns\r\n-#import matplotlib.pyplot as plt\r\n-#from matplotlib.mlab import PCA\r\n-import Tryp_G\r\n-import Tryp_T\r\n-import Tryp_V\r\n-import argparse\r\n-#Entry .sort out the arguments\r\n-\r\n-pdfExport = False\r\n-#parser = argparse.ArgumentParser(description=\'Variant Antigen Profiler - the VAP.\')\r\n-#parser.add_argument(\'name\')\r\n-#parser.add_argument(\'-t\',\'-T\', action = \'store_true\', default = False, help = "Transciptomic Pathway")\r\n-#parser.add_argument(\'-p\',\'-P\', action = \'store_true\', default = False, help = "Export PDFs to HTML directory")\r\n-#parser.add_argument(\'strain\')\r\n-#parser.add_argument(\'Forward_Read_File\')\r\n-#parser.add_argument(\'Reverse_Read_File\')\r\n-#parser.add_argument(\'htmlfile\')\r\n-#parser.add_argument(\'htmlresource\')\r\n-#parser.add_argument(\'heatmapFile\')\r\n-#parser.add_argument(\'PCAFile\')\r\n-#parser.add_argument(\'devheatmapFile\')\r\n-#args = parser.parse_args()\r\n-\r\n-#we have numerous parameters....\r\n-#hard code it for differnt types?\r\n-\r\n-\r\n-arguments = sys.argv\r\n-htmldir = arguments[len(arguments)-1] #last argument is always html_resource\r\n-if not os.path.exists(htmldir):\r\n- os.mkdir(htmldir)\r\n-\r\n-if arguments[1] == \'g_assemble\':\r\n- argdict = {\'name\':2, \'pdfexport\':3, \'kmers\':4,\'inslen\':5, \'covcut\':6, \'forward\':7, \'reverse\':8, \'html_file\':9, \'html_resource\':10}\r\n- Tryp_G.assemble(arguments,argdict)\r\n-if arguments[1] == \'g_contigs\':\r\n- argdict = {\'name\':2, \'pdfexport\':3, \'contigs\':4, \'html_file\':5, \'html_resource\':6}\r\n- Tryp_G.contigs(arguments,argdict)\r\n-if arguments[1] == \'transcipt\':\r\n- argdict = {\'name\':2, \'pdfexport\': 3, \'strain\': 4, \'forward\': 5, \'reverse\': 6, \'html_file\': 7, \'html_resource\': 8}\r\n- Tryp_T.transcriptomicProcess(arguments,argdict)\r\n-if arguments[1] == \'v_assemble\':\r\n- argdict = {\'name\':2, \'pdfexport\':3, \'kmers\':4,\'inslen\':5, \'covcut\':6, \'forward\':7, \'reverse\':8, \'html_file\':9, \'html_resource\':10}\r\n- Tryp_V.vivax_assemble(arguments,argdict)\r\n-if arguments[1] == \'v_contigs\':\r\n- argdict = {\'name\':2, \'pdfexport\':3, \'contigs\':4, \'html_file\':5, \'html_resource\':6}\r\n- Tryp_V.vivax_contigs(arguments,argdict)\r\n-\r\n-\r\n-sys.exit()\r\n-\r\n-\r\n-\r\n-#if not os.path.exists(args.htmlresource):\r\n-# os.mkdir(args.htmlresource)\r\n-#if args.p:\r\n-# pdfExport = True\r\n-#if args.t:\r\n-# print ("Transcriptomic Pathway")\r\n-# Tryp_T.transcriptomicProcess(args.name, pdfExport, args.strain, args.Forward_Read_File, args.Reverse_Read_File, args.htmlfile, args.htmlresource)\r\n-#else:\r\n- #print (\'Genomic Pathway\')\r\n- #Tryp_G.test_output(args.name, args.htmlfile, args.htmlresource, args.heatmapFile, args.PCAFile,args.devheatmapFile)\r\n-# Tryp_G.genomicProcess(args.name, pdfExport, args.Forward_Read_File, args.Reverse_Read_File, args.htmlfile, args.htmlresource)\r\n-\r\n-\r\n+\n+\n+\n+\n+\n+\n+<!DOCTYPE html>\n+<html 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