Exemple #1
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def genDefs(projectPath, projectName, appName, fn_tablesInfo):

    dict_tablesInfo = loadTableInfo(fn_tablesInfo)
    readAppSettAndConnToDb.setupEnvPath(projectPath, projectName)
    organismAppClass = readAppSettAndConnToDb.importAppClassModels(appName)

    genApCode(organismAppClass, dict_tablesInfo)
Exemple #2
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def populateLoci(projectPath, projectName, appName, lociTabFile):

	readAppSettAndConnToDb.setupEnvPath(projectPath, projectName)
	organismDjangoClass = readAppSettAndConnToDb.importAppClassModels(appName)


	dict_chrFileLocs = getChrSeqFilePaths(organismDjangoClass) # multiple paths due to being on multiple chromosomes
	# print(dict_chrFileLocs)

	# dirName_alleleSeqs = readAppSettAndConnToDb.getAlleleFolderName()

	dir_alleles = readAppSettAndConnToDb.importAlleleDirFromSettings(projectName)

	# dir_alleles = dir_alleles + appName + '/'
	# print (dir_alleles)


	dir_alleleSeqsBase = dir_alleles
	dir_alleleSeqsOrg = dir_alleleSeqsBase + appName + "/"
	print (dir_alleleSeqsOrg)

	createFolderIfDoesNotExist(dir_alleleSeqsBase)
	createFolderIfDoesNotExist(dir_alleleSeqsOrg);

	# print (dir_alleleSeqsOrg)
	extractSeqsAndWrite(dict_chrFileLocs, lociTabFile, dir_alleleSeqsOrg, organismDjangoClass)
Exemple #3
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def populateRef(projectPath, projectName, appName, refJsonFile):

    readAppSettAndConnToDb.setupEnvPath(projectPath, projectName)

    appClass = readAppSettAndConnToDb.importAppClassModels(appName)

    jsonObj = readAppSettAndConnToDb.loadJsonFile(refJsonFile)

    dir_reference = readAppSettAndConnToDb.importRefDirFromSettings(
        projectName)

    dir_reference = dir_reference + appName + "/"

    if not os.path.exists(dir_reference):
        os.makedirs(dir_reference)

    refObj = addToTableInOrgDb.addReference(appClass, jsonObj)
    for chromosome in jsonObj["chromosomes"]:
        # print (chromosome)

        chr_fileLoc = cpFileToRightLoc(chromosome['loc_and_filename'],
                                       dir_reference)

        addToTableInOrgDb.addChromosome(appClass, chromosome['number'],
                                        chr_fileLoc, refObj)
Exemple #4
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def addTheHstMatrix(projectPath, projectName, appName, fn_hstMatrix):

    # setting up the appClass
    readAppSettAndConnToDb.setupEnvPath(projectPath, projectName)
    appClass = readAppSettAndConnToDb.importAppClassModels(appName)

    readFileAndAdd(projectPath, appName, appClass, fn_hstMatrix)
Exemple #5
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def addInfo(projectPath, projectName, appName, fn_isolateInfo):

    readAppSettAndConnToDb.setupEnvPath(projectPath, projectName)

    appClass = readAppSettAndConnToDb.importAppClassModels(appName)

    from django.contrib.auth.models import User
    handleTheFile(User, appClass, fn_isolateInfo)
Exemple #6
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def addSchemesToDb(projectPath, projectName, appName, fn_schemesInfo,
                   dir_schemeInfo):

    readAppSettAndConnToDb.setupEnvPath(projectPath, projectName)

    organismAppClass = readAppSettAndConnToDb.importAppClassModels(appName)

    addTheSchemes(organismAppClass, fn_schemesInfo, dir_schemeInfo)
Exemple #7
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def doAddClonalComplexes(projectPath, projectName, appName, ccInfoFile,
                         dir_ccFiles):

    # setting up the appClass
    readAppSettAndConnToDb.setupEnvPath(projectPath, projectName)
    organismAppClass = readAppSettAndConnToDb.importAppClassModels(appName)

    loadAndAddCcs(projectPath, appName, organismAppClass, ccInfoFile,
                  dir_ccFiles)
Exemple #8
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def doAddAllelicProfiles(projectPath, projectName, appName,
                         fn_schemeToApMapping, dir_allelicProfs):

    # setting up the appClass
    readAppSettAndConnToDb.setupEnvPath(projectPath, projectName)
    organismAppClass = readAppSettAndConnToDb.importAppClassModels(appName)

    loadAndAddAps(organismAppClass, fn_schemeToApMapping, dir_allelicProfs,
                  appName, projectPath)
Exemple #9
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def addAlleles(projectPath, projectName, appName, dir_alleleSeqs):

	# setting up the appClass
	readAppSettAndConnToDb.setupEnvPath(projectPath, projectName)
	organismAppClass = readAppSettAndConnToDb.importAppClassModels(appName)

	# print (dir_seqsToSaveTo)
	dir_seqsToSaveTo = readAppSettAndConnToDb.importAlleleDirFromSettings(projectName)

	# for each file in the folder

	extractAndAddAlleles(organismAppClass, dir_alleleSeqs, projectPath, appName, dir_seqsToSaveTo)
Exemple #10
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def genDefs(projectPath, projectName, appName):

	readAppSettAndConnToDb.setupEnvPath(projectPath, projectName)
	organismAppClass = readAppSettAndConnToDb.importAppClassModels(appName)

	genApCode(organismAppClass)
Exemple #11
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def doGen(projectPath, projectName, appName, dbWebsiteUserName):
    readAppSettAndConnToDb.setupEnvPath(projectPath, projectName)
    appClass = readAppSettAndConnToDb.importAppClassModels(appName)

    doThePrinting(appClass, appName, dbWebsiteUserName)