#parser.add_argument("--combineStages" , help= "e.g. <superMat_name1>:<Name1>,<Name2>;<sumperMat_name2>:<Name3>")
parser.add_argument(
"--fo",
help=
"name output figure. Extension indiciates figure type. Data files saved with same name but different extension"
)
#parser.add_argument("--stagesPlot")
parser.add_argument("--vmin", type=float)
parser.add_argument("--vmax", type=float)
parser.add_argument("--linkage_regTargets", default="complete")
parser.add_argument("--linkage_TFs", default="complete")
args = parser.parse_args()
###########################################################################################################################
## LOAD DATA
corrDF = IOutils.loadDF(args.geneCorr)
genes = list(
set().union(*[IOutils.readListFromFile(x) for x in args.genes.split(",")]))
genes_missing = [x for x in genes if not (x in corrDF.index)]
if len(genes_missing) > 0:
print("WARNING the following genes are not in correlation data {}".format(
genes_missing))
genes = [x for x in genes if x in corrDF.index]
TFs = list(
set().union(*[IOutils.readListFromFile(x) for x in args.TFs.split(",")]))
TFs_missing = [x for x in TFs if not (x in corrDF.index)]
if len(TFs_missing) > 0:
print("WARNING the following TFs are not in correlation data {}".format(
TFs_missing))
TFs = [x for x in TFs if x in corrDF.index]
