diff Vap.py @ 0:36cb22bd911d draft

planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Vap.py	Wed Jul 04 16:39:13 2018 -0400
@@ -0,0 +1,91 @@
+"""
+ * Copyright 2018 University of Liverpool
+ * Author: John Heap, Computational Biology Facility, UoL
+ * Based on original scripts of Sara Silva Pereira, Institute of Infection and Global Health, UoL
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ """
+#import subprocess
+#import re
+import os
+import sys
+#import pandas as pd
+#import numpy as np
+#import seaborn as sns
+#import matplotlib.pyplot as plt
+#from matplotlib.mlab import PCA
+import Tryp_G
+import Tryp_T
+import Tryp_V
+import argparse
+#Entry .sort out the arguments
+
+pdfExport = False
+#parser = argparse.ArgumentParser(description='Variant Antigen Profiler - the VAP.')
+#parser.add_argument('name')
+#parser.add_argument('-t','-T', action = 'store_true', default = False, help = "Transciptomic Pathway")
+#parser.add_argument('-p','-P', action = 'store_true', default = False, help = "Export PDFs to HTML directory")
+#parser.add_argument('strain')
+#parser.add_argument('Forward_Read_File')
+#parser.add_argument('Reverse_Read_File')
+#parser.add_argument('htmlfile')
+#parser.add_argument('htmlresource')
+#parser.add_argument('heatmapFile')
+#parser.add_argument('PCAFile')
+#parser.add_argument('devheatmapFile')
+#args = parser.parse_args()
+
+#we have numerous parameters....
+#hard code it for differnt types?
+
+
+arguments = sys.argv
+htmldir = arguments[len(arguments)-1]   #last argument is always html_resource
+if not os.path.exists(htmldir):
+    os.mkdir(htmldir)
+
+if arguments[1] == 'g_assemble':
+    argdict = {'name':2, 'pdfexport':3, 'kmers':4,'inslen':5, 'covcut':6, 'forward':7, 'reverse':8, 'html_file':9, 'html_resource':10}
+    Tryp_G.assemble(arguments,argdict)
+if arguments[1] == 'g_contigs':
+    argdict = {'name':2, 'pdfexport':3, 'contigs':4, 'html_file':5, 'html_resource':6}
+    Tryp_G.contigs(arguments,argdict)
+if arguments[1] == 'transcipt':
+    argdict = {'name':2, 'pdfexport': 3, 'strain': 4, 'forward': 5, 'reverse': 6, 'html_file': 7, 'html_resource': 8}
+    Tryp_T.transcriptomicProcess(arguments,argdict)
+if arguments[1] == 'v_assemble':
+    argdict = {'name':2, 'pdfexport':3, 'kmers':4,'inslen':5, 'covcut':6, 'forward':7, 'reverse':8, 'html_file':9, 'html_resource':10}
+    Tryp_V.vivax_assemble(arguments,argdict)
+if arguments[1] == 'v_contigs':
+    argdict = {'name':2, 'pdfexport':3, 'contigs':4, 'html_file':5, 'html_resource':6}
+    Tryp_V.vivax_contigs(arguments,argdict)
+
+
+sys.exit()
+
+
+
+#if not os.path.exists(args.htmlresource):
+#    os.mkdir(args.htmlresource)
+#if args.p:
+#    pdfExport = True
+#if args.t:
+#    print ("Transcriptomic Pathway")
+#    Tryp_T.transcriptomicProcess(args.name, pdfExport, args.strain, args.Forward_Read_File, args.Reverse_Read_File, args.htmlfile, args.htmlresource)
+#else:
+    #print ('Genomic Pathway')
+    #Tryp_G.test_output(args.name, args.htmlfile, args.htmlresource, args.heatmapFile, args.PCAFile,args.devheatmapFile)
+#    Tryp_G.genomicProcess(args.name, pdfExport, args.Forward_Read_File, args.Reverse_Read_File, args.htmlfile, args.htmlresource)
+
+