def test_generate_group_contigs(self):
cur_dir = os.path.dirname(__file__)
parsed_file_name = os.path.join(cur_dir,"fixtures/parsed_gen_2_2_test.txt")
open_file = open(parsed_file_name, 'r')
groups = read_parsed_taxonomy_file(open_file)
dir_path = os.path.join(cur_dir,"fixtures/reference_genomes")
read_FASTA_files(groups, dir_path)
uniq_id = Uniq_id(10)
group = groups[-1]
s_set = SampleSetting("genomes",20,\
1100,1100,\
True)
sg = SampleGroup(s_set, group, uniq_id)
sg.generate_group_contigs()
assert_equal(len(sg.group.genomes[-1].contigs[-1].full_seq),1100)
assert_equal(len(group.genomes[-1].contigs[-1].full_seq),1100)
assert_equal(len(group.genomes[-1].contigs)+len(group.genomes[0].contigs), 20)
def main(open_name_file, dir_path, x_set, start_position=False):
try:
DNA.generate_kmer_hash(2)
except:
pass
groups = read_parsed_taxonomy_file(open_name_file)
# Read in the FASTA files for each genome
read_FASTA_files(groups,dir_path)
# For each bin, generate a number of contigs,
all_scores = []
id_generator = Uniq_id(1000)
for group_index in range(len(groups)):
group = groups[group_index]
sg = SampleGroup(x_set, group, id_generator)
sg.generate_group_contigs(start_position=start_position)
sg.print_group_contigs(sys.stdout,start_position=start_position)
def test_print_group_contigs(self):
cur_dir = os.path.dirname(__file__)
parsed_file_name = os.path.join(cur_dir,"fixtures/parsed_gen_2_2_test.txt")
open_file = open(parsed_file_name, 'r')
groups = read_parsed_taxonomy_file(open_file)
dir_path = os.path.join(cur_dir,"fixtures/reference_genomes")
read_FASTA_files(groups, dir_path)
uniq_id = Uniq_id(10)
group = groups[-1]
s_set = SampleSetting("genomes",10,\
1100,1100,\
True)
sg = SampleGroup(s_set, group, uniq_id)
sg.generate_group_contigs()
with tempfile.NamedTemporaryFile() as tmp_file:
sg.print_group_contigs(tmp_file)
tmp_file.seek(0)
contig_seqs = list(SeqIO.parse(tmp_file, "fasta"))
assert_equal(len(contig_seqs),10)
assert_equal(contig_seqs[0].id, "Capnocytophaga_canimorsus_Cc5_uid70727_10")
d_string = "Capnocytophaga_canimorsus_Cc5_uid70727_10 Flavobacteriaceae|Capnocytophaga|Capnocytophaga canimorsus"
assert_equal(contig_seqs[0].description, d_string)