diff --git a/bin/prince b/bin/prince index 7d8bf7b..21c8c4d 100755 --- a/bin/prince +++ b/bin/prince @@ -11,7 +11,7 @@ from prince.boost import run_boosts from prince.query_sample import test_target DEFAULT_K = 25 -DEFAULT_BOOST_OUTPUT = resource_filename('prince.resources', 'training_data.txt') +DEFAULT_BOOST_OUTPUT = resource_filename('prince.resources', 'training_data_w_extensions.txt') def main(): parser = argparse.ArgumentParser(description='Prince Options.') diff --git a/prince/tests/test_kmer_generator.py b/prince/tests/test_kmer_generator.py index a60ecb6..7d519df 100644 --- a/prince/tests/test_kmer_generator.py +++ b/prince/tests/test_kmer_generator.py @@ -6,4 +6,6 @@ class KmerGeneratorTest(unittest.TestCase): def test_kmer_generator(self): self.assertEqual(kmer_generator("", 0), {}) - self.assertEqual(kmer_generator("A",1), {0: ['A']}) + self.assertEqual(kmer_generator("A",1), {0: ['A', 'T']}) + self.assertEqual(kmer_generator(["ATTCG","GGGG"],3), {0: ['ATT', 'TTC', 'TCG', 'CGA', 'GAT', 'ATC', 'TCG', 'CGA', 'GAA', 'AAT'], 1: ['GGG', 'GGG', 'GGG', 'GGG', 'CCC', 'CCC', 'CCC', 'CCC']}) + self.assertEqual(kmer_generator(["ATTCG","GGGG"],3, extension=False), {0: ['ATT', 'TTC', 'TCG', 'CGA', 'GAA', 'AAT'], 1: ['GGG', 'GGG', 'CCC', 'CCC']}) diff --git a/training_data_EPs_final.csv b/training_data_EPs_final.csv deleted file mode 100644 index 9981d32..0000000 --- a/training_data_EPs_final.csv +++ /dev/null @@ -1,1920 +0,0 @@ -Beijing391_Extendedprimers_cn:2_125bp_100x,154,0,2,1.35238095238 -Beijing391_Extendedprimers_cn:2_125bp_100x,580,1,2,2.83185840708 -Beijing391_Extendedprimers_cn:2_125bp_100x,960,2,2,3.72164948454 -Beijing391_Extendedprimers_cn:2_125bp_100x,1644,3,2,2.07339449541 -Beijing391_Extendedprimers_cn:2_125bp_100x,2059,4,2,3.62068965517 -Beijing391_Extendedprimers_cn:2_125bp_100x,2531,5,2,1.48205128205 -Beijing391_Extendedprimers_cn:2_125bp_100x,2687,6,2,2.83756345178 -Beijing391_Extendedprimers_cn:2_125bp_100x,2996,7,2,3.28292682927 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