def upload_files():
""" Runs xenoGI."""
MAX_GB_FC = 20
MIN_GB_FC = 3
TREE_FN = "example.tre"
if request.method == 'POST':
treeFile = request.files['newick']
if treeFile and allowed_file(treeFile.filename):
treeFileName = secure_filename(treeFile.filename)
treeFileName = treeFileName.split('.')[0]
now=datetime.datetime.now()
thisFolderName = treeFileName + '-' + str(now.timestamp()).split('.')[0]# timestamp to make unique
#this working directory is the user's "working directory"
current_wd = os.path.join(app.config['WORK_DIRECTORY'], thisFolderName)
os.chdir(WORK_DIRECTORY)
os.system("mkdir "+thisFolderName)
os.chdir(thisFolderName)
treeFile.save(os.path.join(app.config['WORK_DIRECTORY'], thisFolderName, TREE_FN))
#rewrite the parameters file
paramFN = os.path.join(CGI_DIRECTORY, "STARTER_FILES/params.py")
rootFCUserInput= request.form['rootFocal']
paramD = parameters.loadParametersD(paramFN)
paramD['rootFocalClade'] = rootFCUserInput
paramD['fileNameMapFN'] = None
writeParamFile(paramD, paramFN)
#copy starter files over
starter_files = os.path.join(CGI_DIRECTORY, "STARTER_FILES/*")
system_command ="cp "+ starter_files + " " + (os.path.join(app.config['WORK_DIRECTORY'], thisFolderName))
os.system(system_command)
gbffFiles = request.files.getlist("gbff[]")
if (len(gbffFiles) > MAX_GB_FC) or (len(gbffFiles) < MIN_GB_FC) :
return render_template("documentation.html")
else:
#make another directory *ncbi* for the gbfffiles
GENBANK_FD= "ncbi" # this is set in params.py
os.system("mkdir " + GENBANK_FD)
for gbffFile in gbffFiles:
if gbffFile and allowed_file(gbffFile.filename):
gbffFileName = secure_filename(gbffFile.filename)
gbffFile.save(os.path.join(app.config['WORK_DIRECTORY'], thisFolderName, GENBANK_FD, gbffFileName))
# go to the tree files
# work around to be in the right directory
return redirect(url_for('intermediate', tree_fn = thisFolderName))
else: #refer user back to the documentation
return render_template("documentation.html")
else:
return "nope"
import sys
import parameters, genbank, trees, genomes, scores, families, islands
if __name__ == "__main__":
paramFN = sys.argv[1]
paramD = parameters.loadParametersD(paramFN)
## load data structures we'll use below
tree, strainStr2NumD, strainNum2StrD = trees.readTree(paramD['treeFN'])
# an object for gene name conversions
geneNames = genomes.geneNames(paramD['geneOrderFN'], strainStr2NumD,
strainNum2StrD)
subtreeL = trees.createSubtreeL(tree)
subtreeL.sort()
geneOrderT = genomes.createGeneOrderTs(paramD['geneOrderFN'], geneNames,
subtreeL, strainStr2NumD)
## read scores
scoresO = scores.readScores(paramD['scoresFN'], geneNames)
## make gene families
familyIslandFormationSummaryF = open(
paramD['familyIslandFormationSummaryFN'], 'w')
familyL = families.families(
tree, subtreeL, geneNames, scoresO, paramD['minNormThresh'],
paramD['minCoreSynThresh'], paramD['minSynThresh'],
paramD['synAdjustThresh'], paramD['synAdjustExtent'],
paramD['familyFN'], strainNum2StrD, familyIslandFormationSummaryF)
while True:
s=f.readline()
if s == "":
break
nodes = []
for strain in s.split('\t')[1].split(','):
nodes.append(int(strainStr2NumD[strain]))
if strain not in uniqueStrains: uniqueStrains.append(strain)
nodesLL.append(nodes)
return nodesLL,uniqueStrains
if __name__ == "__main__":
#loading parameters from command line that will be used below
paramFN=sys.argv[1]
paramD = parameters.loadParametersD(paramFN)
strainStr = sys.argv[2]
validationFile = sys.argv[3]
minGenes = int(sys.argv[4])
tree,strainStr2NumD,strainNum2StrD = trees.readTree(paramD['treeFN'])
strainNum = strainStr2NumD[strainStr]
#node = strainStr2NumD[strainStr]
# load islands and genes
islandByNodeL=islands.readIslands(paramD['islandOutFN'],tree,strainStr2NumD)
geneNames = genomes.geneNames(paramD['geneOrderFN'],strainStr2NumD,strainNum2StrD)
def upload_files():
""" Runs xenoGI."""
MAX_GB_FC = 20
MIN_GB_FC = 3
TREE_FN = "example.tre"
if request.method == 'POST':
treeFile = request.files['newick']
if treeFile and allowed_file(treeFile.filename):
treeFileName = secure_filename(treeFile.filename)
treeFileName = treeFileName.split('.')[0]
now = datetime.datetime.now()
thisFolderName = treeFileName + '-' + str(
now.timestamp()).split('.')[0] # timestamp to make unique
#this working directory is the user's "working directory"
current_wd = os.path.join(app.config['WORK_DIRECTORY'],
thisFolderName)
os.chdir(WORK_DIRECTORY)
os.system("mkdir " + thisFolderName)
os.system("chmod ugo+rwx " + thisFolderName)
os.chdir(thisFolderName)
treeFile.save(
os.path.join(app.config['WORK_DIRECTORY'], thisFolderName,
TREE_FN))
#rewrite the parameters file from the xenoGI/examples/params.py
paramDefaultFile = os.path.join(XENO_GI_DIRECTORY, "example",
"params.py")
thisFolderPath = os.path.join(WORK_DIRECTORY, thisFolderName)
os.system("cp " + paramDefaultFile + " " + ".")
paramFN = os.path.join(thisFolderPath, "params.py")
paramD = parameters.loadParametersD(paramFN)
paramD[
'fileNameMapFN'] = None # we assume the user does not have a human to gbff file mapping
#if you want to add another parameter
# then add additional line to form, following "rootFocal"
# 1) update template/forms.html
# 2) copy requst.forms[<parameter_name>]
# 3) overwrite the paramD (loaded file from xenoGI/example/params.py)
rootFCUserInput = request.form['rootFocal'] # copy this line
paramD[
'rootFocalClade'] = rootFCUserInput # copy this line too - changing the value
writeParamFile(paramD, paramFN) #rewrites paramFN
gbffFiles = request.files.getlist("gbff[]")
if (len(gbffFiles) > MAX_GB_FC) or (len(gbffFiles) < MIN_GB_FC):
return render_template("documentation.html")
else:
#make another directory *ncbi* for the gbfffiles
GENBANK_FD = "ncbi" # this is set in params.py
os.system("mkdir " + GENBANK_FD)
for gbffFile in gbffFiles:
if gbffFile and allowed_file(gbffFile.filename):
gbffFileName = secure_filename(gbffFile.filename)
gbffFile.save(
os.path.join(app.config['WORK_DIRECTORY'],
thisFolderName, GENBANK_FD,
gbffFileName))
os.system("chmod ugo+rwx " + thisFolderName + "/ncbi/*")
os.system("chmod ugo+rwx " + thisFolderName + "/*")
# go to the tree files
# work around to be in the right directory
return redirect(url_for('intermediate', tree_fn=thisFolderName))
else: #refer user back to the documentation
return render_template("documentation.html")
else:
return "nope"