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authorzsloan2015-03-27 20:28:51 +0000
committerzsloan2015-03-27 20:28:51 +0000
commitd0911a04958a04042da02a334ccc528dae79cc17 (patch)
tree3c48e2e937c1dbeaf00a5697c87ed251afa5c8f1 /web/webqtl/cmdLine/webqtlCmdLine.py
parenta840ad18e1fe3db98a359a159e9b9b72367a2839 (diff)
downloadgenenetwork2-d0911a04958a04042da02a334ccc528dae79cc17.tar.gz
Removed everything from 'web' directory except genofiles and renamed the directory to 'genotype_files'
Diffstat (limited to 'web/webqtl/cmdLine/webqtlCmdLine.py')
-rwxr-xr-xweb/webqtl/cmdLine/webqtlCmdLine.py176
1 files changed, 0 insertions, 176 deletions
diff --git a/web/webqtl/cmdLine/webqtlCmdLine.py b/web/webqtl/cmdLine/webqtlCmdLine.py
deleted file mode 100755
index ebc10e1c..00000000
--- a/web/webqtl/cmdLine/webqtlCmdLine.py
+++ /dev/null
@@ -1,176 +0,0 @@
-# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
-#
-# This program is free software: you can redistribute it and/or modify it
-# under the terms of the GNU Affero General Public License
-# as published by the Free Software Foundation, either version 3 of the
-# License, or (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# See the GNU Affero General Public License for more details.
-#
-# This program is available from Source Forge: at GeneNetwork Project
-# (sourceforge.net/projects/genenetwork/).
-#
-# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
-# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
-#
-#
-#
-# This module is used by GeneNetwork project (www.genenetwork.org)
-#
-# Created by GeneNetwork Core Team 2010/08/10
-#
-# Last updated by GeneNetwork Core Team 2010/10/20
-
-
-
-########################################################
-#XZ, Aug 10, 2010
-#This part is the temporary solution to make python be able to find other subpackages.
-#We can't set global environment because there are many branches on the development machine.
-
-import sys, os
-
-current_file_name = __file__
-pathname = os.path.dirname( current_file_name )
-abs_path = os.path.abspath(pathname)
-sys.path.insert(0, abs_path + '/..')
-
-########################################################
-
-
-
-import traceback
-import string
-import cPickle
-
-from base import webqtlConfig
-from base.templatePage import templatePage
-from utility import webqtlUtil
-
-
-if __name__ == "__main__":
- try:
- if len(sys.argv) > 2:
- getID = string.lower(sys.argv[1])
- else:
- raise ValueError
-
- cmdtype = sys.argv[1]
- sessionfile = sys.argv[2]
-
- fd = None
-
- fp = open(os.path.join(webqtlConfig.TMPDIR, sessionfile + '.session'), 'rb')
- fd = cPickle.load(fp)
- fp.close()
-
- if cmdtype == "heatmap":
- from heatmap import heatmapPage
- reload(heatmapPage)
- page = heatmapPage.heatmapPage(fd)
- page.writeFile(sessionfile+'.html')
- elif cmdtype == "directplot":
- from pairScan import DirectPlotPage
- reload(DirectPlotPage)
- page = DirectPlotPage.DirectPlotPage(fd)
- page.writeFile(sessionfile+'.html')
- elif cmdtype == "networkGraph":
- from networkGraph import networkGraphPage
- reload(networkGraphPage)
- page = networkGraphPage.networkGraphPage(fd)
- page.writeFile(sessionfile+'.html')
- elif cmdtype == "interval":
- from intervalMapping import IntervalMappingPage
- reload(IntervalMappingPage)
- page = IntervalMappingPage.IntervalMappingPage(fd)
- page.writeFile(sessionfile+'.html')
- elif cmdtype == "correlation":
- from correlation import CorrelationPage
- reload (CorrelationPage)
- page = CorrelationPage.CorrelationPage(fd)
- page.writeFile(sessionfile+'.html')
- elif cmdtype == "partialCorrelation":
- from correlation import PartialCorrDBPage
- reload(PartialCorrDBPage)
- page = PartialCorrDBPage.PartialCorrDBPage(fd)
- page.writeFile(sessionfile+'.html')
- elif cmdtype == "correlationComparison":
- from compareCorrelates import multitrait
- reload(multitrait)
- page = multitrait.compCorrPage(fd)
- page.writeFile(sessionfile+'.html')
- elif cmdtype == "genreport": # Generate Report Page
- spacer = '</TR></Table><Table width=900 cellSpacing=0 cellPadding=5><TR>'
-
- from basicStatistics import BasicStatisticsPage
- reload(BasicStatisticsPage)
- page1 = BasicStatisticsPage.BasicStatisticsPage(fd)
-
- if not fd.formdata.getvalue('bsCheck'):
- page1.dict['body'] = ""
-
- if fd.formdata.getvalue('tcCheck'):
- from correlation import CorrelationPage
- reload(CorrelationPage)
- page2 = CorrelationPage.CorrelationPage(fd)
- page1.dict['body'] += spacer + str(page2.dict['body'])
- page1.dict['js1'] += page2.dict['js1']
-
- if fd.formdata.getvalue('imCheck'):
- from intervalMapping import IntervalMappingPage
- reload(IntervalMappingPage)
- page3 = IntervalMappingPage.IntervalMappingPage(fd)
- page1.dict['body'] += spacer + str(page3.dict['body'])
-
- if fd.formdata.getvalue('mrCheck'):
- from markerRegression import MarkerRegressionPage
- reload(MarkerRegressionPage)
- page4 = MarkerRegressionPage.MarkerRegressionPage(fd)
- page1.dict['body'] += spacer + str(page4.dict['body'])
-
- if fd.formdata.getvalue('psCheck'):
- from pairScan import DirectPlotPage
- reload(DirectPlotPage)
- page5 = DirectPlotPage.DirectPlotPage(fd)
- page1.dict['body'] += spacer + str(page5.dict['body'])
-
- page1.writeFile(sessionfile+'.html')
-
- elif cmdtype == "genreport2": # Generate Report Page v2
- spacer = '</TR></Table><Table width=900 cellSpacing=0 cellPadding=5><TR>'
-
- from basicStatistics import BasicStatisticsPage_alpha
- reload(BasicStatisticsPage_alpha)
- page1 = BasicStatisticsPage_alpha.BasicStatisticsPage_alpha(fd)
- page1.writeFile(sessionfile+'.html')
- elif cmdtype == "snpbrowser":
- from snpBrowser import snpBrowserPage
- reload(snpBrowserPage)
- page = snpBrowserPage.snpBrowserPage(fd)
- page.writeFile(sessionfile+'.html')
- elif cmdtype == "QTLminer":
- from qtlminer import QTLminer
- reload(QTLminer)
- page = QTLminer.QTLminer(fd)
- page.writeFile(sessionfile+'.html')
- elif cmdtype == "tissueCorrelation":
- from correlationMatrix import TissueCorrelationPage
- reload(TissueCorrelationPage)
- page = TissueCorrelationPage.TissueCorrelationPage(fd)
- page.writeFile(sessionfile+'.html')
- elif cmdtype == "markerRegression":
- from markerRegression import MarkerRegressionPage
- reload(MarkerRegressionPage)
- page = MarkerRegressionPage.MarkerRegressionPage(fd)
- page.writeFile(sessionfile+'.html')
- else:
- raise ValueError
- except:
- fp = open(os.path.join(webqtlConfig.TMPDIR, sessionfile +'.html'), 'wb')
- fp.write('\n\n<pre>')
- traceback.print_exc(file=fp)
- fp.write('\n</pre>')
- fp.close()