def testIgnoreIL(self):
peptides = set()
peptides.add("GLL")
peptides_to_proteins = protein_annotator.map_peptides_to_proteins(
peptides, self.testfile, ignore_il=False)
self.assertEqual(25, len(peptides_to_proteins["GLL"]))
peptides_to_proteins = protein_annotator.map_peptides_to_proteins(
peptides, self.testfile, ignore_il=True)
self.assertEqual(46, len(peptides_to_proteins["GLL"]))
def testProteinInference(self):
return
peptides = set()
peptides.add("GLL")
peptides_to_proteins = protein_annotator.map_peptides_to_proteins(
peptides, self.testfile)
peptide_map = protein_annotator.do_protein_inference(
peptides_to_proteins)
self.assertEqual(1, len(peptide_map))
self.assertTrue("GLL" in peptide_map)
self.assertEqual(24, peptide_map["GLL"][0].count(";"))
# add another unique peptide
peptides.add("EEWQCLDTAQRNLYKNV")
peptides_to_proteins = protein_annotator.map_peptides_to_proteins(
peptides, self.testfile)
peptide_map = protein_annotator.do_protein_inference(
peptides_to_proteins)
self.assertEqual(2, len(peptide_map))
self.assertEqual("M0QXM7", peptide_map["EEWQCLDTAQRNLYKNV"][0])
self.assertEqual("M0QXM7", peptide_map["GLL"][0])
def testMapPeptides(self):
peptides = set()
peptides.add("KWVTFISLLLL")
peptides.add("AGGE")
peptides.add("LLA")
peptides.add("A")
protein_map = protein_annotator.map_peptides_to_proteins(
peptides, self.testfile)
self.assertEqual(len(peptides), len(protein_map))
for sequence in protein_map.keys():
org_len = len(protein_map[sequence])
unique_len = len(set(protein_map[sequence]))
self.assertEqual(unique_len, org_len)