annotate commons/core/writer/test/Test_MapWriter.py @ 6:769e306b7933

Change the repository level.

from SMART.Java.Python.structure.Transcript import Transcript
from SMART.Java.Python.structure.Interval import Interval
import unittest
import os
from SMART.Java.Python.misc import Utils
from commons.core.writer.MapWriter import MapWriter
from commons.core.utils.FileUtils import FileUtils

class Test_MapWriter(unittest.TestCase):
    
    def setUp(self):
        self.expFileName = "expMapWriter.map"
        self.obsFileName = "testMapWriter1.map"
        
    def tearDown(self):
        os.remove(self.expFileName)
        os.remove(self.obsFileName)
        
    def test_writer(self):
        self.write_ExpMapFileName()
        writer = MapWriter(self.obsFileName)
        
        transcript = Transcript()
        transcript.setName("test1.1")
        transcript.setChromosome("arm_X")
        transcript.setStart(1000)
        transcript.setEnd(4000)
        transcript.setDirection("+")
        transcript.setTagValue("ID", "test1.1-1")
        transcript.setTagValue("occurrence", 1)
        transcript.setTagValue("nbOccurrences", 2)
        
        exon1 = Interval()
        exon1.setChromosome("arm_X")
        exon1.setStart(1000)
        exon1.setEnd(2000)
        exon1.setDirection("+")
        
        exon2 = Interval()
        exon2.setChromosome("arm_X")
        exon2.setStart(3000)
        exon2.setEnd(4000)
        exon2.setDirection("+")
        
        transcript.addExon(exon1)
        transcript.addExon(exon2)
        
        writer.addTranscript(transcript)
        writer.write()
        writer.close()
        
        self.assertTrue(FileUtils.are2FilesIdentical(self.expFileName, self.obsFileName))
        

    def write_ExpMapFileName(self):
        f = open(self.expFileName, "w")
        f.write("test1.1\tarm_X\t1000\t4001\n")
        f.close()

if __name__ == '__main__':
    unittest.main()