+
+
+
+
+
+
+
+
+
+
+ Permalink
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Join GitHub today
+GitHub is home to over 36 million developers working together to host and review code, manage projects, and build software together.
+ Sign up +
+
+
+
+
+
+
+
+
+
+
+ Find file
+
+
+ Copy path
+
+
+
+ + VAPPER-Galaxy/Vap.py +
+ +
+
+ Find file
+
+
+ Copy path
+
+
+
+ Fetching contributors…
+
+
+
+ 
+ Cannot retrieve contributors at this time
+
+
+ Cannot retrieve contributors at this time
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ | + | """ | +
| + | * 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 Tryp_V_T | +
| + | 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) | +
| + | if arguments[1] == 'v_transcript': | +
| + | argdict = {'name':2, 'pdfexport': 3, 'refFastq': 4, 'forward': 5, 'reverse': 6, 'html_file': 7, 'html_resource': 8} | +
| + | Tryp_V_T.transcriptomicProcess(arguments,argdict) | +
| + | + | +
| + | + | +
| + | sys.exit() | +
| + | + | +