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import sys
sys.path.insert(0, '../src/')
import os
import shutil
import unittest
import os
import numpy
from transit_test import *
import pytransit.norm_tools as norm_tools
import pytransit.tnseq_tools as tnseq_tools
import pytransit.stat_tools as stat_tools
import pytransit.transit_tools as transit_tools
class TestTnSeqTools(TransitTestCase):
def test_read_data(self):
data,position = tnseq_tools.get_data(all_data_list)
K,N = data.shape
self.assertEqual(K, 5)
self.assertGreater(N, 70000)
def test_genes_creation_fromwig(self):
G = tnseq_tools.Genes(all_data_list, annotation)
N = len(G)
test_orf = "Rv0001"
test_name = "dnaA"
#Test list creation
self.assertGreater(N, 3000)
#Test dictionary lookup + data
self.assertEqual(G[test_orf].orf, test_orf)
self.assertEqual(G[test_orf].name, test_name)
#Test list lookup + data
self.assertEqual(G[0].orf, test_orf)
self.assertEqual(G[0].name, test_name)
def test_genes_creation_fromdata(self):
data,position = tnseq_tools.get_data(all_data_list)
Kreps,Nsites = data.shape
G = tnseq_tools.Genes([], annotation, data=data, position=position)
N = len(G)
test_orf = "Rv0001"
test_name = "dnaA"
#Test list creation
self.assertGreater(N, 3000)
#Test dictionary lookup + data
self.assertEqual(G[test_orf].orf, test_orf)
self.assertEqual(G[test_orf].name, test_name)
#Test list lookup + data
self.assertEqual(G[0].orf, test_orf)
self.assertEqual(G[0].name, test_name)
def test_file_types(self):
types = tnseq_tools.get_file_types(all_data_list)
types = set(types)
self.assertEqual(len(types), 1)
self.assertTrue("himar1" in types)
#
def test_normalization(self):
N = len(all_data_list)
data,position = tnseq_tools.get_data(all_data_list)
norm_data,factors = norm_tools.normalize_data(data, "TTR")
self.assertFalse((factors == numpy.ones(N)).all())
#
def test_cleanargs_negative_arguments(self):
TEST_RAWARGS = ["test", "-p", "-10"]
args, kwargs = transit_tools.cleanargs(TEST_RAWARGS)
self.assertEqual(int(kwargs.get("p",0)), -10)
#
def test_cleanargs_flag_without_arguments(self):
TEST_RAWARGS = ["test", "-p"]
args, kwargs = transit_tools.cleanargs(TEST_RAWARGS)
self.assertTrue(kwargs.get("p",False))
#
def test_cleanargs_positional_arguments(self):
TEST_RAWARGS = ["a", "b", "c", "-d", "1", "e"]
args, kwargs = transit_tools.cleanargs(TEST_RAWARGS)
self.assertEqual(args, ["a", "b", "c", "e"])
#
def test_cleanargs_positional_arguments_w_quotes(self):
TEST_RAWARGS = ["a", "b", "c", "-d", "1", "test this"]
args, kwargs = transit_tools.cleanargs(TEST_RAWARGS)
self.assertEqual(args, ["a", "b", "c", "test this"])
#
def test_cleanargs_flag_arguments_w_quotes(self):
TEST_RAWARGS = ["a", "b", "c", "-d", "1", "-p", "test this"]
args, kwargs = transit_tools.cleanargs(TEST_RAWARGS)
self.assertEqual(kwargs.get("p"), "test this")
#
def test_cleanargs_flag_arguments_with_double_dash(self):
TEST_RAWARGS = ["a", "b", "c", "-d", "1", "--p", "test this"]
args, kwargs = transit_tools.cleanargs(TEST_RAWARGS)
self.assertFalse("p" in kwargs)
self.assertFalse("--p" in kwargs)
self.assertTrue("-p" in kwargs)
if __name__ == '__main__':
unittest.main()
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