def create_personal_results(mapping_fp,
distance_matrix_fp,
collated_dir_fp,
output_fp, prefs_fp,
personal_id_field,
otu_table,
parameter_fp,
personal_ids=None,
column_title='Self',
individual_titles=None,
category_to_split='BodySite',
time_series_category='WeeksSinceStart',
suppress_alpha_rarefaction=False,
verbose=False):
map_as_list, header, comments = parse_mapping_file(open(mapping_fp, 'U'))
try:
personal_id_index = header.index(personal_id_field)
except ValueError:
raise ValueError("personal id field (%s) is not a mapping file column header" %
personal_id_field)
header.append(column_title)
if personal_ids == None:
personal_ids = get_personal_ids(map_as_list, personal_id_index)
else:
for id in personal_ids.split(','):
if id not in get_personal_ids(map_as_list, personal_id_index):
raise ValueError('%s is not an id in the mapping file.' %id)
personal_ids = personal_ids.split(',')
output_directories = []
makedirs(output_fp)
otu_table_title = otu_table.split('/')[-1].split('.')
for person_of_interest in personal_ids:
makedirs(join(output_fp, person_of_interest))
pcoa_dir = join(output_fp, person_of_interest, "beta_diversity")
rarefaction_dir = join(output_fp, person_of_interest, "alpha_rarefaction")
area_plots_dir = join(output_fp, person_of_interest, "time_series")
output_directories.append(pcoa_dir)
output_directories.append(rarefaction_dir)
output_directories.append(area_plots_dir)
personal_mapping_file_fp = join(output_fp, person_of_interest, "mapping_file.txt")
html_fp = join(output_fp, person_of_interest, "index.html")
personal_map = create_personal_mapping_file(map_as_list,
header,
comments,
person_of_interest,
personal_mapping_file_fp,
personal_id_index,
individual_titles)
create_index_html(person_of_interest, html_fp)
column_title_index = header.index(column_title)
column_title_values = set([e[column_title_index] for e in personal_map])
cat_index = header.index(category_to_split)
cat_values = set([e[cat_index] for e in personal_map])
## Alpha rarefaction steps
if not suppress_alpha_rarefaction:
cmd = "make_rarefaction_plots.py -i %s -m %s -p %s -o %s" % (collated_dir_fp,
personal_mapping_file_fp,
prefs_fp,
rarefaction_dir)
if verbose:
print cmd
stdout, stderr, return_code = qiime_system_call(cmd)
if return_code != 0:
raise ValueError("Command failed!\nCommand: %s\n Stdout: %s\n Stderr: %s\n" %\
(cmd, stdout, stderr))
## Beta diversity steps
cmd = "make_3d_plots.py -m %s -p %s -i %s -o %s" % (personal_mapping_file_fp,
prefs_fp,
distance_matrix_fp,
pcoa_dir)
if verbose:
print cmd
stdout, stderr, return_code = qiime_system_call(cmd)
if return_code != 0:
raise ValueError("Command failed!\nCommand: %s\n Stdout: %s\n Stderr: %s\n" %\
(cmd, stdout, stderr))
## Split OTU table into self/other per-body-site tables
cmd = "split_otu_table.py -i %s -m %s -f %s -o %s" % (otu_table,
personal_mapping_file_fp,
column_title,
area_plots_dir)
if verbose:
print cmd
stdout, stderr, return_code = qiime_system_call(cmd)
if return_code != 0:
raise ValueError("Command failed!\nCommand: %s\n Stdout: %s\n Stderr: %s\n" %\
(cmd, stdout, stderr))
for column_title_value in column_title_values:
print column_title_value
biom_fp = join(area_plots_dir, '%s_%s.%s' % (otu_table_title[0], column_title_value, otu_table_title[1]))
body_site_dir = join(area_plots_dir, column_title_value)
cmd = "split_otu_table.py -i %s -m %s -f %s -o %s" % (biom_fp,
personal_mapping_file_fp,
category_to_split,
body_site_dir)
if verbose:
print cmd
stdout, stderr, return_code = qiime_system_call(cmd)
if return_code != 0:
raise ValueError("Command failed!\nCommand: %s\n Stdout: %s\n Stderr: %s\n" %\
(cmd, stdout, stderr))
for cat_value in cat_values:
otu_table_fp = join(body_site_dir, "otu_table_%s_%s.biom" % (column_title_value, cat_value))
print otu_table_fp
if exists(otu_table_fp):
# Not supporting parameter files yet
#if parameter_fp == None:
# parameter_fp = ''
#else:
# parameter_fp = '-p %s' %parameter_fp
plots = join(area_plots_dir, "taxa_plots_%s_%s" % (column_title_value, cat_value))
cmd = "summarize_taxa_through_plots.py -i %s -o %s -c %s -m %s -s" % (otu_table_fp,
plots,
time_series_category,
personal_mapping_file_fp)
#parameter_fp)
if verbose:
print cmd
stdout, stderr, return_code = qiime_system_call(cmd)
if return_code != 0:
raise ValueError("Command failed!\nCommand: %s\n Stdout: %s\n Stderr: %s\n" %\
(cmd, stdout, stderr))
return output_directories
def create_personal_results(mapping_fp,
distance_matrix_fp,
collated_dir_fp,
output_fp, prefs_fp,
personal_id_field,
personal_ids=None,
column_title=None,
individual_titles=None):
map_as_list, header, comments = parse_mapping_file(open(mapping_fp, 'U'))
try:
personal_id_index = header.index(personal_id_field)
except ValueError:
raise ValueError("personal id field (%s) is not a mapping file column header" %
personal_id_field)
if column_title == None:
header.append('Self')
else:
header.append(column_title)
if personal_ids == None:
personal_ids = get_personal_ids(map_as_list, personal_id_index)
else:
for id in personal_ids.split(','):
if id not in get_personal_ids(map_as_list, personal_id_index):
raise ValueError('%s is not an id in the mapping file.' %id)
personal_ids = personal_ids.split(',')
output_directories = []
makedirs(output_fp)
for person_of_interest in personal_ids:
makedirs(join(output_fp, person_of_interest))
pcoa_dir = join(output_fp, person_of_interest, "beta_diversity")
rarefaction_dir = join(output_fp, person_of_interest, "alpha_rarefaction")
output_directories.append(pcoa_dir)
output_directories.append(rarefaction_dir)
personal_mapping_file_fp = join(output_fp, person_of_interest, "mapping_file.txt")
html_fp = join(output_fp, person_of_interest, "index.html")
create_personal_mapping_file(map_as_list,
header,
comments,
person_of_interest,
personal_mapping_file_fp,
personal_id_index,
individual_titles)
create_index_html(person_of_interest, html_fp)
cmd = "make_rarefaction_plots.py -i %s -m %s -p %s -o %s" % (collated_dir_fp,
personal_mapping_file_fp,
prefs_fp,
rarefaction_dir)
stdout, stderr, return_code = qiime_system_call(cmd)
if return_code != 0:
raise ValueError("Command failed!\nCommand: %s\n Stdout: %s\n Stderr: %s\n" %\
(cmd, stdout, stderr))
cmd = "make_3d_plots.py -m %s -p %s -i %s -o %s" % (personal_mapping_file_fp,
prefs_fp,
distance_matrix_fp,
pcoa_dir)
stdout, stderr, return_code = qiime_system_call(cmd)
if return_code != 0:
raise ValueError("Command failed!\nCommand: %s\n Stdout: %s\n Stderr: %s\n" %\
(cmd, stdout, stderr))
return output_directories
