def test_main_signature_subtraction(self):
cur_dir = os.path.dirname(__file__)
parsed_file_name = os.path.join(cur_dir,"fixtures/parsed_gen_only_2.txt")
contig_file_name = os.path.join(cur_dir,"fixtures/identical_contigs_different_genomes.fna")
taxonomy_input_file = open(parsed_file_name,'r')
contig_input_file = open(contig_file_name,'r')
kmer_length = 3
dir_path = os.path.join(cur_dir,"fixtures/reference_genomes")
with tempfile.NamedTemporaryFile() as tmp_file:
with RedirectStdStreams(stdout=tmp_file):
score_contigs_multinomial.main(contig_input_file,taxonomy_input_file, dir_path,kmer_length)
tmp_file.seek(0)
num_lines = sum(1 for line in tmp_file)
# #contigs * #genomes + #header
# 2*2+1=5
assert_equal(num_lines,5)
tmp_file.seek(0)
header_line = tmp_file.readline()
all_entries = tmp_file.read()
entries = all_entries.strip().split("\n")
scores = [line.split("\t")[0] for line in entries]
first_contig_first_genome = scores[0]
first_contig_second_genome = scores[1]
second_contig_first_genome = scores[2]
second_contig_second_genome = scores[3]
contig_id_differ1 = float(first_contig_first_genome) - float(second_contig_first_genome)
assert_equal(abs(contig_id_differ1)>0,True)
contig_id_differ2 = float(first_contig_second_genome) - float(second_contig_second_genome)
assert_equal(abs(contig_id_differ2)>0,True)
def test_main(self):
cur_dir = os.path.dirname(__file__)
parsed_file_name = os.path.join(cur_dir,"fixtures/parsed_gen_2_2_test.txt")
contig_file_name = os.path.join(cur_dir,"fixtures/generated_contigs_test.fna")
taxonomy_input_file = open(parsed_file_name,'r')
contig_input_file = open(contig_file_name,'r')
kmer_length = 3
dir_path = os.path.join(cur_dir,"fixtures/reference_genomes")
dir_structure = 'tree_structure'
with tempfile.NamedTemporaryFile() as tmp_file:
with RedirectStdStreams(stdout=tmp_file):
score_contigs_multinomial.main(contig_input_file,taxonomy_input_file, dir_path,kmer_length,dir_structure)
tmp_file.seek(0)
num_lines = sum(1 for line in tmp_file)
# #contigs * #genomes + #header
# 29*7+1=204
assert_equal(num_lines,204)
tmp_file.seek(0)
header_line = tmp_file.readline()
first_data_line = tmp_file.readline()
elements =first_data_line.strip().split("\t")
real_elements = ['Anaplasmataceae', 'Ehrlichia', 'Ehrlichia canis', 'Ehrlichia_canis_Jake_uid58071', 'Anaplasmataceae', 'Ehrlichia', 'Ehrlichia canis', 'Ehrlichia_canis_Jake_uid58071', '1000']
assert_equal(real_elements, elements[1:])
