def main(args): file_species_pairs = [] i = 1 while i < len(args)-2: file_species_pairs.append([args[i], args[i+1]]) i += 2 cutoff = float(sys.argv[-2]) plot_dir = sys.argv[-1] species2elms = {} for file, species in file_species_pairs: species2elms[species] = utils.get_seq2count_dict(file, cutoff) elms = {} for species in species2elms: for elm in species2elms[species]: elms[elm] = True for elm in elms: if utils.check_ones(species2elms, elm) and (elm in species2elms['swine'] or elm in species2elms['human'] or elm in species2elms['chicken']) and elm in species2elms['H_sapiens'] : utils_plot.elm_host_barplot(species2elms, elm, os.path.join(plot_dir, elm + '.hosts.png'))
def main(args): file_species_pairs = [] i = 1 while i < len(args)-2: file_species_pairs.append([args[i], args[i+1]]) i += 2 cutoff = float(sys.argv[-2]) plot_dir = sys.argv[-1] species2elms = {} virus2elms = {} # first grab virus ELMs for file, species in file_species_pairs: if file.find('flu') != -1: virus2elms[species] = utils.get_seq2count_dict(file, cutoff) else: species2elms[species] = True elms = {} for species in virus2elms: for elm in virus2elms[species]: elms[elm] = True for species in species2elms: species2elms[species] = utils.get_seq2count_dict_for_seqs(file, cutoff, virus2elms) for virus in virus2elms: species2elms[virus] = virus2elms[virus] for elm in elms: if utils.check_ones(species2elms, elm): if utils_distance.distance_elms(species2elms['Sus_scrofa'][elm], species2elms['H_sapiens'][elm]) > float(-1) or utils_distance.distance_elms(species2elms['Sus_scrofa'][elm], species2elms['Gallus_gallus'][elm]) > float(0): utils_plot.elm_host_barplot(species2elms, elm, os.path.join(plot_dir, elm + '.virus_hosts.png'))