import gzip
import os
import tempfile
import unittest

import lightmotif

SEQUENCE = "ATGTCCCAACAACGATACCCCGAGCCCATCGCCGTCATCGGCTCGGCATGCAGATTCCCAGGCG"
EXPECTED = [
    -23.07094,
    -18.678621,
    -15.219191,
    -17.745737,
    -18.678621,
    -23.07094,
    -17.745737,
    -19.611507,
    -27.463257,
    -29.989803,
    -14.286304,
    -26.53037,
    -15.219191,
    -10.826873,
    -10.826873,
    -22.138054,
    -38.774437,
    -30.922688,
    -5.50167,
    -24.003826,
    -18.678621,
    -15.219191,
    -35.315006,
    -17.745737,
    -10.826873,
    -30.922688,
    -23.07094,
    -6.4345555,
    -31.855574,
    -23.07094,
    -15.219191,
    -31.855574,
    -8.961102,
    -26.53037,
    -27.463257,
    -14.286304,
    -15.219191,
    -26.53037,
    -23.07094,
    -18.678621,
    -14.286304,
    -18.678621,
    -26.53037,
    -16.152077,
    -17.745737,
    -18.678621,
    -17.745737,
    -14.286304,
    -30.922688,
    -18.678621,
]


class TestScanner(unittest.TestCase):
    def test_scan(self):
        motif = lightmotif.create(["GTTGACCTTATCAAC", "GTTGATCCAGTCAAC"])
        frequencies = motif.counts.normalize(0.1)
        pssm = frequencies.log_odds()

        seq = lightmotif.stripe(SEQUENCE)

        hits = list(lightmotif.scan(pssm, seq))
        self.assertEqual(len(hits), 0)

        hits = list(lightmotif.scan(pssm, seq, threshold=-10.0))
        self.assertEqual(len(hits), 3)
        
        hits.sort(key=lambda h: h.position)
        self.assertAlmostEqual(hits[0].score, -5.50167, places=5)
        self.assertAlmostEqual(hits[1].score, -6.4345555, places=5)
        self.assertAlmostEqual(hits[2].score, -8.961102, places=5)