def genDefs(projectPath, projectName, appName, fn_tablesInfo): dict_tablesInfo = loadTableInfo(fn_tablesInfo) readAppSettAndConnToDb.setupEnvPath(projectPath, projectName) organismAppClass = readAppSettAndConnToDb.importAppClassModels(appName) genApCode(organismAppClass, dict_tablesInfo)
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)
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)
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)
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)
def addSchemesToDb(projectPath, projectName, appName, fn_schemesInfo, dir_schemeInfo): readAppSettAndConnToDb.setupEnvPath(projectPath, projectName) organismAppClass = readAppSettAndConnToDb.importAppClassModels(appName) addTheSchemes(organismAppClass, fn_schemesInfo, dir_schemeInfo)
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)
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)
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)
def genDefs(projectPath, projectName, appName): readAppSettAndConnToDb.setupEnvPath(projectPath, projectName) organismAppClass = readAppSettAndConnToDb.importAppClassModels(appName) genApCode(organismAppClass)
def doGen(projectPath, projectName, appName, dbWebsiteUserName): readAppSettAndConnToDb.setupEnvPath(projectPath, projectName) appClass = readAppSettAndConnToDb.importAppClassModels(appName) doThePrinting(appClass, appName, dbWebsiteUserName)