def main():
#Get the parameters from the command line, using printInfo() as a fallback
#Minimun 2 parameters: [0] = name file python, [1] = name file of the list of the gene (.csv/.zip)
if len(sys.argv) >= 2:
if sys.argv[1] == '--help':
ut.printInfo()
elif sys.argv[1] == '-vitis':
#read parameters
cmd = ut.readParameters(sys.argv)
#print(type(cmd[1]))
#build matrix of genes
matrixGenes = vitis.buildMatrixGenesVitis(cmd[0], cmd[1])
#print(matrixGenes)
print('Build matrix successfully', flush=True)
#build graph of interaction between genes
print("Building complete graph...", flush=True)
graphGenes = ut.manageDuplicates(ut.buildGraph(matrixGenes))
print('Build graph successufully', flush=True)
#find core of graphGenes
print("Searching core network...", flush=True)
coreGraph = ut.findCoreGraph(graphGenes)
print('Core find successufully', flush=True)
#print in output complete graph and core
vitis.printOutput(coreGraph, graphGenes)
else:
print('ERROR: Need 1 parameters')
print(
'Usage: python3 managerList.py -vitis [FILTERS]... -files [FILES]...'
)
else:
print('ERROR: wrong format')
ut.printInfo()
def applyFilter(listGenes, filter):
if filter[0] == '-f' and len(filter) == 2:
listGenes = filters.filterFrel(listGenes, float(filter[1]))
global min_frel
min_frel = float(filter[1])
elif filter[0] == '-t' and len(filter) >= 2:
listGenes = filters.filterType(listGenes, filter[1:])
elif filter[0] == '-a' and len(filter) == 1:
global autoSaveImg
autoSaveImg = True
else:
print('ERROR: incorrect parameters filter')
ut.printInfo()
return listGenes
def applyFilter(listGenes, filter):
if filter[0] == '-f' and len(filter) == 2:
listGenes = filters.filterFrel(listGenes, float(filter[1]))
global min_frel
min_frel = float(filter[1])
elif filter[0] == '-t':
print('ERROR: incorrect parameters filter. -t only for Vitis')
ut.printInfo()
elif filter[0] == '-a' and len(filter) == 1:
global autoSaveImg
autoSaveImg = True
elif filter[0] == '-i' and len(filter) == 2:
global ignoreEdgesIsoform
ignoreEdgesIsoform = True
if filter[1] == 'comp':
global comprimeNode
comprimeNode = True
elif filter[1] != 'notcomp':
print('ERROR: incorrect parameters filter -i')
ut.printInfo()
#elif other filter
else:
print('ERROR: incorrect parameters filter')
ut.printInfo()
return listGenes
def main():
#Get the parameters from the command line, using printInfo() as a fallback
#Minimun 2 parameters: [0] = name file python, [1] = name file of the list of the gene (.csv/.zip)
if len(sys.argv) >= 2:
if sys.argv[1] == '--help':
ut.printInfo()
elif sys.argv[1] == '-vitis':
#read parameters
cmd = ut.readParameters(sys.argv)
#build matrix of genes
matrixGenes = vitis.buildMatrixGenesVitis(cmd[0], cmd[1])
print('Build matrix successfully', flush=True)
#build graph of interaction between genes
print("Building complete graph...", flush=True)
graphGenes = ut.manageDuplicates(ut.buildGraph(matrixGenes))
print('Build graph successufully', flush=True)
#find core of graphGenes
print("Searching core network...", flush=True)
coreGraph = ut.findCoreGraph(graphGenes)
print('Core find successufully', flush=True)
#print in output complete graph and core
vitis.printOutput(coreGraph, graphGenes)
elif sys.argv[1] == '-human':
#check the DB
fantom = False
if sys.argv[2] == '-fantom':
pass# fantom = True
elif sys.argv[2] == '-TCGA':
pass
else:
print('ERROR: need to specify -fantom or -TCGA')
ut.printInfo()
#read parameters
cmd = ut.readParameters(sys.argv)
#build matrix of genes
matrixGenes = human.buildMatrixGenesHuman(cmd[0], cmd[1], fantom)
print('Build matrix successfully', flush=True)
#build graph of interaction between genes
print("Building complete graph...", flush=True)
graphGenes = ut.manageDuplicates(human.removeIsoformEdges(ut.buildGraph(matrixGenes[0])))
graphGenesOld = []
if matrixGenes[2]:
graphGenesOld = ut.manageDuplicates(ut.buildGraph(matrixGenes[1]))
print('Build graph successufully', flush=True)
#find core of graphGenes
print("Searching core network...", flush=True)
coreGraph = ut.findCoreGraph(graphGenes)
print('Core find successufully', flush=True)
#print in output complete graph and core
human.printOutput(coreGraph, graphGenes, graphGenesOld)
else:
print('ERROR: Need 1 parameters')
print('Usage: python3 managerList.py PARAM [FILTERS]... -files [FILES]...')
print('PARAM:')
print('\t-vitis\tLists of vitis')
print('\t-human\tLists of human')
else:
print('ERROR: wrong format')
ut.printInfo()