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+arguments = sys.argv
+htmldir = arguments[len(arguments)-1] #last argument is always html_resource
+if not os.path.exists(htmldir):
+ os.mkdir(htmldir)
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- - VAPPER-Galaxy/Vap.py -
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+sys.exit()
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- 81 lines (72 sloc)
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- 3.04 KB
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+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)
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- | - | """ | -
| - | * 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() | -
| - | - | -