def read_parsed_taxonomy_file(open_name_file):
groups = []
# Read the file with all names, divide them into groups
for line in open_name_file:
if line[0:12] == 'family_name:':
family = line.split('\t')[1].strip()
elif line[0:11] == 'genus_name:':
genus = line.split('\t')[1].strip()
new_group = GenomeGroup(genus)
new_group.family = family
groups.append(new_group)
elif line[0:6] == 'entry:':
genome_name = line.split('\t')[2].strip()
genome_species = line.split('\t')[1].strip()
meta_genome = {'id': genome_name,
'species': genome_species,
'genus': genus,
'family': family,
'file_name': genome_name
}
groups[-1].genome_data.append(meta_genome)
return groups
def main(open_name_file, dir_path, kmer_length, x_set):
groups = []
DNA.generate_kmer_hash(kmer_length)
# Read the file with all names, divide them into groups
for line in open_name_file:
if line[0:12] == 'family_name:':
family = line.split('\t')[1].strip()
elif line[0:11] == 'genus_name:':
genus = line.split('\t')[1].strip()
new_group = GenomeGroup(genus)
new_group.family = family
groups.append(new_group)
elif line[0:6] == 'entry:':
genome_name = line.split('\t')[2].strip()
genome_species = line.split('\t')[1].strip()
meta_genome = {'id': genome_name,
'species': genome_species,
'genus': genus,
'family': family,
'file_name': genome_name
}
groups[-1].genome_data.append(meta_genome)
# Each genome in a group is a bin, fit parameters to all bins
os.chdir(dir_path)
for group in groups:
for genome_data in group.genome_data:
dir_name = genome_data['file_name']
fasta_files = os.listdir(dir_name)
for fasta_file in fasta_files:
genome_file = open(dir_name + '/' + fasta_file)
identifier = genome_file.readline()
# Only use non-plasmid genomes
# Some bacterial genomes contain more than 1 chromosonme,
# but assumed not more than 2
if identifier.find('plasmid') == -1 and identifier.find('chromosome 2') == -1:
genome_file.close() #Close and reopen the same file
genome_file = open(dir_name + '/' + fasta_file)
genome_seq = list(SeqIO.parse(genome_file, "fasta"))
if len(genome_seq) > 1:
sys.stderr.write("Warning! The file " + fasta_file + " in directory " + dir_name + " contained more than one sequence, ignoring all but the first!" + os.linesep)
genome = DNA(id = dir_name, seq= str(genome_seq[0].seq))
genome.calculate_signature()
genome.genus = genome_data['genus']
genome.species = genome_data['species']
genome.family = genome_data['family']
group.genomes.append(genome)
genome_file.close()
# For each bin, generate a number of contigs,
# re-calculate parameters for that bin without contig-section.
# Further score this contig against all bins, keep within-group
# scores separate from outside-group scores.
all_scores = []
id_generator = Uniq_id(1000)
for group_index in range(len(groups)):
group = groups[group_index]
rest_groups = all_but_index(groups, group_index)
test = Experiment(x_set, group, rest_groups, id_generator)
group_scores = test.execute()
all_scores.append(group_scores)
sys.stdout.write("p_value\tcontig_family\tcontig_genus\tcontig_species\tcontig_genome\tcompare_family\tcompare_genus\tcompare_species\tcompare_genome\tcontig_id" + os.linesep)
for group_scores in all_scores:
for genome_scores in group_scores:
for score in genome_scores:
sys.stdout.write(str(score) + '\n')
