cistematic/experiments/__init__.py

   1 ###########################################################################
   2 #                                                                         #
   3 # C O P Y R I G H T   N O T I C E                                         #
   4 #  Copyright (c) 2003-10 by:                                              #
   5 #    * California Institute of Technology                                 #
   6 #                                                                         #
   7 #    All Rights Reserved.                                                 #
   8 #                                                                         #
   9 # Permission is hereby granted, free of charge, to any person             #
  10 # obtaining a copy of this software and associated documentation files    #
  11 # (the "Software"), to deal in the Software without restriction,          #
  12 # including without limitation the rights to use, copy, modify, merge,    #
  13 # publish, distribute, sublicense, and/or sell copies of the Software,    #
  14 # and to permit persons to whom the Software is furnished to do so,       #
  15 # subject to the following conditions:                                    #
  16 #                                                                         #
  17 # The above copyright notice and this permission notice shall be          #
  18 # included in all copies or substantial portions of the Software.         #
  19 #                                                                         #
  20 # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,         #
  21 # EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF      #
  22 # MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND                   #
  23 # NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS     #
  24 # BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN      #
  25 # ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN       #
  26 # CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE        #
  27 # SOFTWARE.                                                               #
  28 ###########################################################################
  29 #
  30 try:
  31     from pysqlite2 import dbapi2 as sqlite
  32 except:
  33     from sqlite3 import dbapi2 as sqlite
  34
  35 __all__ = ["analyzeMotifs", "experiment", "locate",  "phyloFoot", "phyloTest",
  36            "randomset", "simple", "varyLength",  "orthology"]
  37
  38 experimentTypes = [("simple", "Simple"), ("fasta", "Fasta"), ("locate", "Locate"),
  39                    ("varyLength", "VaryLength"), ("phyloFoot", "PhyloFoot"),
  40                    ("phyloTest", "PhyloTest"), ("orthology", "Orthology"),
  41                    ("experiment", "generic")]
  42
  43 webExperimentTypes = [("simple", "Simple"), ("orthology", "Orthology")]
  44
  45
  46 def loadExperiment(expID, expFilePath, analysisID="default", conservationID="default", consDB=""):
  47     newExp = ""
  48     try:
  49         db = sqlite.connect(expFilePath)
  50         sql = db.cursor()
  51         sql.execute('select data from settings where expID = :expID and settingName = "experimentType"', locals())
  52         expType = str(sql.fetchone()[0])
  53         sql.close()
  54         db.close()
  55         expClass = ""
  56         for etype in experimentTypes:
  57             if etype[0] == expType:
  58                 expClass = etype[1]
  59
  60         if expClass != "":
  61             importString = "from %s import %s" % (expType, expClass)
  62             exec importString
  63             expString = 'newExp = %s("%s","%s")' % (expClass, expID, expFilePath)
  64             exec expString
  65         else:
  66             print "Could not find associated class for %s" % expType
  67     except:
  68         print "Could not load experiment %s from database %s " % (expID, expFilePath)
  69
  70     if consDB == "":
  71         consDB = expFilePath
  72     try:
  73         expString = 'newExp.loadAnalysis("%s")' % analysisID
  74         exec expString
  75         print "loaded analysis %s" % analysisID
  76         expString = "newExp.loadConservation('%s', '%s')" % (conservationID, consDB)
  77         exec expString
  78         print "loaded conservation %s" % conservationID
  79     except:
  80         pass
  81
  82     return newExp
  83
  84
  85 def listExperiments(expFilePath):
  86     result = []
  87     try:
  88         db = sqlite.connect(expFilePath)
  89         sql = db.cursor()
  90         sql.execute('select distinct expID, data from settings where settingName = "experimentType" ')
  91         data = sql.fetchall()
  92         sql.close()
  93         db.close()
  94         for (expID, expType) in data:
  95             result.append((str(expID), str(expType)))
  96     except:
  97         print "Could not list experiments in database %s " % (expFilePath)
  98
  99     return result