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src/m/o/MotifAnalysisPackage-0.0.1/motifStatistics/motif.py   MotifAnalysisPackage(Download)
    # Creating PWM from pseudocounted input
    pwmFile = open(tempFileName,"r")
    pwm = Motif.read(pwmFile,"jaspar-pfm")
    pwmFile.close()
    os.system("rm "+tempFileName)

src/s/e/seriesoftubes-0.9.6.9/bioplus/sitefinder.py   seriesoftubes(Download)
 
    if type(motif) is str:
        motif = Bio.Motif.read(open(motif), motif_type)
 
    # start the output file

src/b/i/biopython-1.63/Tests/test_Motif.py   biopython(Download)
    def test_pfm_parsing(self):
        """Test to be sure that Motif can parse pfm  files.
        """
        motif= Motif.read(self.PFMin, "jaspar-pfm")
        self.assertEqual(motif.length, 12)
 
    def test_sites_parsing(self):
        """Test to be sure that Motif can parse sites files.
        """
        motif= Motif.read(self.SITESin, "jaspar-sites")
    def setUp(self):
        handle = open("Motif/SRF.pfm")
        self.m = Motif.read(handle, "jaspar-pfm")
        handle.close()
        self.s = Seq("ACGTGTGCGTAGTGCGT", self.m.alphabet)

src/b/i/biopython-HEAD/Tests/test_Motif.py   biopython(Download)
    def test_pfm_parsing(self):
        """Test to be sure that Motif can parse pfm  files.
        """
        motif= Motif.read(self.PFMin, "jaspar-pfm")
        self.assertEqual(motif.length, 12)
 
    def test_sites_parsing(self):
        """Test to be sure that Motif can parse sites files.
        """
        motif= Motif.read(self.SITESin, "jaspar-sites")
    def setUp(self):
        handle = open("Motif/SRF.pfm")
        self.m = Motif.read(handle, "jaspar-pfm")
        handle.close()
        self.s = Seq("ACGTGTGCGTAGTGCGT", self.m.alphabet)