Esempio n. 1
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def main(args):
    suffix = sys.argv[1]
    elms = sys.argv[2:]
    file_species_pairs = []
    for g in global_settings.GENOMES:
        file_species_pairs.append(('results/elmdict_'
                                   + g + suffix, g))
    plot_dir = 'plots/for_aydin/'

    species2elms = {}
    for file, species in file_species_pairs:
        species2elms[species] = utils.get_seq2count_dict(file, float(0))

    for elm in elms:
        utils_plot.elm_host_barplot(species2elms, elm,
                                    os.path.join(plot_dir,
                                                 elm + '.hosts' 
                                                 + suffix + '.png'))
Esempio n. 2
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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'))
Esempio n. 3
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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'))
Esempio n. 4
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                dis[g] = utils_distance.distance_elms(species2dict[g][elm],
                                                      virus2dict[v][elm])
            is_less = True
            is_gtr = True
            for g in genomes:
                if g != v2h[v]:
                    if dis[v2h[v]] > dis[g]:#it is not less than at least one
                        is_less = False
            if is_less:
                right_count[v] += 1
            new_d = {}
            for h in species2dict:
                new_d[h] = species2dict[h]
            for v in virus2dict:
                new_d[v] = virus2dict[v]
            utils_plot.elm_host_barplot(new_d, 
                                        elm, elm + '.png')


for v in right_count:
    print v, right_count[v]

            
#for elm in use_elms:
#    utils_plot.elm_host_barplot(virus2dict, elm, elm + '.png')

# v = 'human'
# for elm in use_elms:
#     if elm in host_elms:
#         dis = {}
#         for g in genomes:
#             dis[g] = utils_distance.distance_elms(species2dict[g][elm],
Esempio n. 5
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import utils, utils_plot, utils_distance

d = {'web':utils.get_seq2count_dict('results/human.website.elm.elmdict',
                                    float(.01)),
     'regex':utils.get_seq2count_dict('results/hprd_new.regex.elms.elmdict',
                                      float(.01))}
elms = utils_distance.get_elements(d['web'], d['regex'])

for elm in elms:
    utils_plot.elm_host_barplot(d, elm, 'plots/hprd/' + elm + '.png')