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add xms parsing test
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committed by
Peter Cock
parent
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commit
70f6347afa
102
Tests/motifs/abdb.xms
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102
Tests/motifs/abdb.xms
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<motif>
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<name>Abd-B</name>
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</weightmatrix>
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<prop>
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<key>PMID</key>
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<value>7914870</value>
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</prop>
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<prop>
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<key>PWM_type</key>
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<value>selex</value>
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</prop>
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<prop>
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<key>Transfac_ID</key>
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<value>M00090</value>
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</prop>
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<threshold>0.0</threshold>
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</motif>
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@ -24,6 +24,7 @@ class MotifTestsBasic(unittest.TestCase):
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self.PFMin = open("motifs/SRF.pfm")
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self.SITESin = open("motifs/Arnt.sites")
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self.CLUSTERBUSTERin = open("motifs/clusterbuster.pfm")
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self.XMSin = open("motifs/abdb.xms")
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self.TFout = "motifs/tf.out"
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self.FAout = "motifs/fa.out"
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self.PFMout = "motifs/fa.out"
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@ -414,6 +415,13 @@ class MotifTestsBasic(unittest.TestCase):
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self.CLUSTERBUSTERin.seek(0)
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self.assertEqual(motifs.write(record, "clusterbuster").split(), self.CLUSTERBUSTERin.read().split())
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def test_xms_parsing(self):
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"""Test if Bio.motifs can parse and output xms PFM files."""
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record = motifs.parse(self.XMSin, "xms")
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self.assertEqual(len(record), 1)
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self.assertEqual(record[0].name, "Abd-B")
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self.assertEqual(record[0].length, 14)
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def test_pfm_parsing(self):
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"""Test if Bio.motifs can parse JASPAR-style pfm files."""
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m = motifs.read(self.PFMin, "pfm")
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