gseapy/gsea.py
def prepare_outdir(self):
        """create temp directory."""
        self._outdir = self.outdir
        if self._outdir is None:
            self._tmpdir = TemporaryDirectory()
            self.outdir = self._tmpdir.name
        elif isinstance(self.outdir, str):
            mkdirs(self.outdir)
        else:
            raise Exception("Error parsing outdir: %s"%type(self.outdir))

        # handle gmt type
        if isinstance(self.gene_sets, str):
            _gset = os.path.split(self.gene_sets)[-1].lower().rstrip(".gmt")
        elif isinstance(self.gene_sets, dict):
            _gset = "blank_name"
        else:
            raise Exception("Error parsing gene_sets parameter for gene sets")

        logfile = os.path.join(self.outdir, "gseapy.%s.%s.log" % (self.module, _gset))
        return logfile
def prepare_outdir(self):
        """create temp directory."""
        self._outdir = self.outdir
        if self._outdir is None:
            self._tmpdir = TemporaryDirectory()
            self.outdir = self._tmpdir.name
        elif isinstance(self.outdir, str):
            mkdirs(self.outdir)
        else:
            raise Exception("Error parsing outdir: %s"%type(self.outdir))

        # handle gmt type
        if isinstance(self.gene_sets, str):
            _gset = os.path.split(self.gene_sets)[-1].lower().rstrip(".gmt")
        elif isinstance(self.gene_sets, dict):
            _gset = "blank_name"
        else:
            raise Exception("Error parsing gene_sets parameter for gene sets")

        logfile = os.path.join(self.outdir, "gseapy.%s.%s.log" % (self.module, _gset))
        return logfile
def prepare_outdir ( self ) : self . _outdir = self . outdir if self . _outdir is None : self . _tmpdir = TemporaryDirectory ( ) self . outdir = self . _tmpdir . name elif isinstance ( self . outdir , str ) : mkdirs ( self . outdir ) else : raise Exception ( "Error parsing outdir: %s" % type ( self . outdir ) ) # handle gmt type if isinstance ( self . gene_sets , str ) : _gset = os . path . split ( self . gene_sets ) [ - 1 ] . lower ( ) . rstrip ( ".gmt" ) elif isinstance ( self . gene_sets , dict ) : _gset = "blank_name" else : raise Exception ( "Error parsing gene_sets parameter for gene sets" ) logfile = os . path . join ( self . outdir , "gseapy.%s.%s.log" % ( self . module , _gset ) ) return logfile
create temp directory.
create temp directory .