def main(open_name_file, dir_path,l):
DNA.generate_kmer_hash(1)
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,group in enumerate(groups):
for genome in group.genomes:
parts = genome.split_seq(l)
print_parts(parts,sys.stdout, id_generator, genome)
def test_print_parts(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)
with tempfile.NamedTemporaryFile() as tmp_file:
for group_index, group in enumerate(groups):
for genome in group.genomes:
parts = genome.split_seq(10000)
print_parts(parts,tmp_file,uniq_id, genome)
tmp_file.seek(0)
genome_parts = list(SeqIO.parse(tmp_file,"fasta"))
assert_equal(len(genome_parts),1788)
assert_equal(genome_parts[0].id,"Ehrlichia_canis_Jake_uid58071_10_0")
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)
def test_read_single_FASTA_file(self):
cur_dir = os.path.dirname(__file__)
parsed_file_name = os.path.join(cur_dir,"fixtures/parsed_gen_0_0_mock_test_complete.txt")
open_file = open(parsed_file_name, 'r')
groups = read_parsed_taxonomy_file(open_file)
dir_path = os.path.join(cur_dir,"fixtures/mock_references_test.fa")
output = read_FASTA_files(groups, dir_path, dir_structure='single_fasta_file')
assert_is_none(output)
last_genome = groups[-1].genomes[-1]
assert_equal(len(last_genome.full_seq),2222430) #wrong length
assert_equal(last_genome.id, "Pyrobaculum_aerophilum_str._IM2")
# Same family and genera within group
assert_equal(groups[-1].genomes[-1].family, groups[-1].genomes[0].family)
assert_equal(groups[-1].genomes[-1].genus, groups[-1].genomes[0].genus)
# A correct family
assert_equal(groups[-1].genomes[-1].family, "Thermoproteaceae") # wrong family
def test_read_FASTA_files(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")
output = read_FASTA_files(groups, dir_path)
assert_is_none(output)
last_genome = groups[-1].genomes[-1]
assert_equal(len(last_genome.full_seq),2612925)
assert_equal(last_genome.id, "Capnocytophaga_ochracea_DSM_7271_uid59197")
# Same family and genera within group
assert_equal(groups[-1].genomes[-1].family, groups[-1].genomes[0].family)
assert_equal(groups[-1].genomes[-1].genus, groups[-1].genomes[0].genus)
# A correct family
assert_equal(groups[-1].genomes[-1].family, "Flavobacteriaceae")