comparison commons/core/seq/test/Test_Bioseq.py @ 18:94ab73e8a190

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17:b0e8584489e6

import os
import sys
from commons.core.seq.Bioseq import Bioseq 
from commons.core.utils.FileUtils import FileUtils
from commons.core.coord.Map import Map


class Test_Bioseq( unittest.TestCase ):
    
    def setUp(self):

        expNucl = 'N'
        obsNucl = bioseq.getATGCNFromIUPAC('Z')
        self.assertEquals(expNucl, obsNucl)
        
        
    def test_partialIUPAC(self):
        bioseq = Bioseq()
        bioseq.sequence = "ATGCNRATGCN"
        expSequence1 = "ATGCNAATGCN"
        expSequence2 = "ATGCNGATGCN"

18:94ab73e8a190

import os
import sys
from commons.core.seq.Bioseq import Bioseq 
from commons.core.utils.FileUtils import FileUtils
from commons.core.coord.Map import Map
from commons.core.checker.RepetException import RepetException


class Test_Bioseq( unittest.TestCase ):
    
    def setUp(self):

        expNucl = 'N'
        obsNucl = bioseq.getATGCNFromIUPAC('Z')
        self.assertEquals(expNucl, obsNucl)
        
        
    def test_getATGCNFromIUPACandATGCN(self):
        self.assertEquals("G", Bioseq().getATGCNFromIUPACandATGCN('R', 'A'))
        self.assertEquals("A", Bioseq().getATGCNFromIUPACandATGCN('R', 'G'))
        self.assertEquals("C", Bioseq().getATGCNFromIUPACandATGCN('Y', 'T'))
        self.assertEquals("T", Bioseq().getATGCNFromIUPACandATGCN('Y', 'C'))
        self.assertEquals("C", Bioseq().getATGCNFromIUPACandATGCN('M', 'A'))
        self.assertEquals("A", Bioseq().getATGCNFromIUPACandATGCN('M', 'C'))
        self.assertEquals("T", Bioseq().getATGCNFromIUPACandATGCN('K', 'G'))
        self.assertEquals("G", Bioseq().getATGCNFromIUPACandATGCN('K', 'T'))
        self.assertEquals("A", Bioseq().getATGCNFromIUPACandATGCN('W', 'T'))
        self.assertEquals("T", Bioseq().getATGCNFromIUPACandATGCN('W', 'A'))
        self.assertEquals("G", Bioseq().getATGCNFromIUPACandATGCN('S', 'C'))
        self.assertEquals("C", Bioseq().getATGCNFromIUPACandATGCN('S', 'G'))
        
    def test_getATGCNFromIUPACandATGCN_invalid_combination(self):
        obsMsg = ""
        try:
            Bioseq().getATGCNFromIUPACandATGCN('R', 'T')
        except RepetException as e:
            obsMsg = e.getMessage()
            
        self.assertEqual("IUPAC code 'R' and nucleotide 'T' are not compatible", obsMsg)
        
    def test_getATGCNFromIUPACandATGCN_invalid_IUPAC(self):
        bioseq = Bioseq()
        obsMsg = ""
        try:
            bioseq.getATGCNFromIUPACandATGCN('B', 'T')
        except RepetException as e:
            obsMsg = e.getMessage()
            
        self.assertEqual("Can't retrieve the third nucleotide from IUPAC code 'B' and nucleotide 'T'", obsMsg)
        
    def test_partialIUPAC(self):
        bioseq = Bioseq()
        bioseq.sequence = "ATGCNRATGCN"
        expSequence1 = "ATGCNAATGCN"
        expSequence2 = "ATGCNGATGCN"