def addTheHstMatrix(projectPath, projectName, appName, mgtlist): # setting up the appClass readAppSettAndConnToDb.setupEnvPath(projectPath, projectName) appClass = readAppSettAndConnToDb.importAppClassModels(appName) readFileAndAdd(projectPath, appName, appClass, mgtlist)
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 doAddClonalComplexes(projectPath, projectName, appName, tableNum_orderNum,
schemeName, cc, st, dst, merges):
# setting up the appClass
readAppSettAndConnToDb.setupEnvPath(projectPath, projectName)
organismAppClass = readAppSettAndConnToDb.importAppClassModels(appName)
# print(organismAppClass)
loadAndAddCcs(projectPath, appName, organismAppClass, tableNum_orderNum,
schemeName, cc, st, dst, merges)
def addSnpMutsToDb(projectPath, projectName, orgAppName, allele_dict):
# setting up the appClass
readAppSettAndConnToDb.setupEnvPath(projectPath, projectName)
organismAppClass = readAppSettAndConnToDb.importAppClassModels(orgAppName)
# running add snps
for locus in allele_dict:
allele = allele_dict[locus][1]
snplist = allele_dict[locus][3]
getAlleleAndAddSnpsTo_(organismAppClass, {}, locus, allele, snplist)
def addAlleles(projectPath, projectName, appName,dir_alleleSeqs, alleles_out_dict):
## change dir_alleleSeqs to use alleles_dict_out
# setting up the appClass
readAppSettAndConnToDb.setupEnvPath(projectPath, projectName)
organismAppClass = readAppSettAndConnToDb.importAppClassModels(appName)
dir_seqsToSaveTo = readAppSettAndConnToDb.importAlleleDirFromSettings(projectName)
# print(organismAppClass,dir_seqsToSaveTo)
# for each file in the folder
extractAndAddAlleles(organismAppClass, dir_alleleSeqs, projectPath, appName, alleles_out_dict)
def addApForScheme(projectPath, projectName, appName, schemeName, profile_dict,
st, dst, nodash_to_dash):
readAppSettAndConnToDb.setupEnvPath(projectPath, projectName)
orgAppClass = readAppSettAndConnToDb.importAppClassModels(appName)
list_tableNameClass = getTableClasses(orgAppClass, schemeName, appName,
projectPath)
schObj = getFromTableInOrgDb.getScheme(orgAppClass, schemeName)
lociNames_sorted = getLociNamesSorted(schObj)
# print("HELLO",len(lociNames_sorted))
# print(list_tableNameClass)
locus_ids_list_o_lists = list(chunks(lociNames_sorted, 1000))
alleles_ls = []
for locuslis in locus_ids_list_o_lists:
nlis = []
for locus in locuslis:
locus = nodash_to_dash[locus]
nlis.append(profile_dict[locus])
alleles_ls.append(nlis)
# print("1")
# for i in locus_ids_list_o_lists:
# print(len(i),i)
# print("2")
# for i in alleles_ls:
# print(len(i), i)
#for addToDb() need lociNames_sorted = list of lists of loci ids = [[l1,l2,l3...][l1001,l1002....]]
# also need equivalent list of allele assignments = alleles_ls = [[1,2,1,...][-1_1,4,....]]
#TODO check when adding that allele + locus ids are used NOT unique allele id...
# print("pre addToDb")
# print(st, dst, locus_ids_list_o_lists)
addToDb(list_tableNameClass, st, dst, locus_ids_list_o_lists, alleles_ls)
def genDefs(projectPath, projectName, appName):
readAppSettAndConnToDb.setupEnvPath(projectPath, projectName)
organismAppClass = readAppSettAndConnToDb.importAppClassModels(appName)
genApCode(organismAppClass)