view SMART/Java/Python/test/Test_F_RestrictFromCoverage.py @ 31:0ab839023fe4

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import unittest
import os, os.path
from optparse import OptionParser
from SMART.Java.Python.misc import Utils
from SMART.Java.Python.structure.Transcript import Transcript
from commons.core.writer.Gff3Writer import Gff3Writer
from commons.core.parsing.GffParser import GffParser
from SMART.Java.Python.RestrictFromCoverage import RestrictFromCoverage

REFERENCE = 0
QUERY     = 1

class Test_F_Clusterize(unittest.TestCase):

    def setUp(self):
        self._queryFileName     = "testQuery.gff3"
        self._refFileName       = "testRef.gff3"
        self._outputFileName    = "output.gff3"
        self._parsers           = {QUERY: Gff3Writer(self._queryFileName, 0), REFERENCE: Gff3Writer(self._refFileName, 0)}
        self._writeQuery()
        
    def tearDown(self):
        for file in (self._queryFileName, self._refFileName, self._outputFileName):
            if os.path.exists(file):
                os.remove(file)

    def _writeQuery(self):
        self._addTranscript(QUERY, 1, 1000, 2000, "+")
        self._parsers[QUERY].close()

    def _writeReferences(self, values):
        for value in values:
            self._addTranscript(REFERENCE, value["cpt"], value["start"], value["end"], value["strand"])
        self._parsers[REFERENCE].close()

    def _addTranscript(self, type, cpt, start, end, strand):
        t = Transcript()
        t.setChromosome("chr1")
        t.setName("test%d" % (cpt))
        t.setStart(start)
        t.setEnd(end)
        t.setDirection(strand)
        self._parsers[type].addTranscript(t)

    def _checkTranscript(self, transcript, start, end, strand):
        self.assertEquals(transcript.getStart(),     start)
        self.assertEquals(transcript.getEnd(),       end)
        self.assertEquals(transcript.getDirection(), strand)

    def _startTool(self, minNucleotides = None, maxNucleotides = None, minPercent = None, maxPercent = None, minOverlap = None, maxOverlap = None, strands = False):
        rfc = RestrictFromCoverage(0)
        rfc.setInputFileName(self._queryFileName, "gff3", QUERY)
        rfc.setInputFileName(self._refFileName,   "gff3", REFERENCE)
        rfc.setOutputFileName(self._outputFileName)
        rfc.setNbNucleotides(minNucleotides, maxNucleotides)
        rfc.setPercent(minPercent, maxPercent)
        rfc.setOverlap(minOverlap, maxOverlap)
        rfc.setStrands(strands)
        rfc.run()
        return GffParser(self._outputFileName, 0)

    def test_simple(self):
        self._writeReferences([{"cpt": 1, "start": 1000, "end": 2000, "strand": "+"}])
        parser = self._startTool()
        self.assertEquals(parser.getNbTranscripts(), 1)
        for transcript in parser.getIterator():
            self._checkTranscript(transcript, 1000, 2000, 1)

    def test_nbOverlapsMin_pos(self):
        self._writeReferences([{"cpt": 1, "start": 1000, "end": 2000, "strand": "+"}, {"cpt": 2, "start": 1000, "end": 2000, "strand": "+"}])
        parser = self._startTool(1, None, None, None, 2)
        self.assertEquals(parser.getNbTranscripts(), 1)
        for transcript in parser.getIterator():
            self._checkTranscript(transcript, 1000, 2000, 1)

    def test_nbOverlapsMin_neg(self):
        self._writeReferences([{"cpt": 1, "start": 1000, "end": 2000, "strand": "+"}])
        parser = self._startTool(1, None, None, None, 2)
        self.assertEquals(parser.getNbTranscripts(), 0)

    def test_nbOverlapsMax_pos(self):
        self._writeReferences([{"cpt": 1, "start": 1000, "end": 2000, "strand": "+"}])
        parser = self._startTool(1, None, None, None, None, 1)
        self.assertEquals(parser.getNbTranscripts(), 1)
        for transcript in parser.getIterator():
            self._checkTranscript(transcript, 1000, 2000, 1)

    def test_nbOverlapsMax_neg(self):
        self._writeReferences([{"cpt": 1, "start": 1000, "end": 2000, "strand": "+"}, {"cpt": 2, "start": 1000, "end": 2000, "strand": "+"}])
        parser = self._startTool(1, None, None, None, None, 1)
        self.assertEquals(parser.getNbTranscripts(), 0)

    def test_nbNucleotidesMin_pos(self):
        self._writeReferences([{"cpt": 1, "start": 1000, "end": 1100, "strand": "+"}])
        parser = self._startTool(100, None, None, None, 1)
        self.assertEquals(parser.getNbTranscripts(), 1)
        for transcript in parser.getIterator():
            self._checkTranscript(transcript, 1000, 2000, 1)

    def test_nbNucleotidesMin_neg(self):
        self._writeReferences([{"cpt": 1, "start": 1000, "end": 1100, "strand": "+"}])
        parser = self._startTool(200, None, None, None, 1)
        self.assertEquals(parser.getNbTranscripts(), 0)

    def test_PercentMin_pos(self):
        self._writeReferences([{"cpt": 1, "start": 1000, "end": 1500, "strand": "+"}])
        parser = self._startTool(None, None, 50, None, 1)
        self.assertEquals(parser.getNbTranscripts(), 1)
        for transcript in parser.getIterator():
            self._checkTranscript(transcript, 1000, 2000, 1)

    def test_PercentMin_neg(self):
        self._writeReferences([{"cpt": 1, "start": 1000, "end": 1500, "strand": "+"}])
        parser = self._startTool(None, None, 100, None, 1)
        self.assertEquals(parser.getNbTranscripts(), 0)

    def test_NoStrand_neg(self):
        self._writeReferences([{"cpt": 1, "start": 1000, "end": 1500, "strand": "-"}])
        parser = self._startTool(1, None, None, None, 1)
        self.assertEquals(parser.getNbTranscripts(), 1)

    def test_strand_pos(self):
        self._writeReferences([{"cpt": 1, "start": 1000, "end": 1500, "strand": "+"}])
        parser = self._startTool(1, None, None, None, 1, None, True)
        self.assertEquals(parser.getNbTranscripts(), 1)

    def test_strand_neg(self):
        self._writeReferences([{"cpt": 1, "start": 1000, "end": 1500, "strand": "-"}])
        parser = self._startTool(1, None, None, None, 1, None, True)
        self.assertEquals(parser.getNbTranscripts(), 0)

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