def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
map_fp = opts.mapping
biom_fp = opts.biom_file
min_seqs_sample = opts.min_seqs_sample
subject_category = opts.subject_name
cleaned_fp = opts.clean_fp
verbose = opts.verbose
map_data, headers, comments = parse_mapping_file(open(map_fp, 'U'))
biom_table = parse_biom_table(open(biom_fp, 'U'))
# getting valid samples from biom file
real_map_headers, real_map_data = filter_mapping_file(map_data, headers,\
biom_table.SampleIds, include_repeat_cols=False)
if subject_category not in real_map_headers:
raise ValueError, 'This column: %s is not in the mapping file, try %s'%\
(subject_category, real_map_headers)
sorted_counts_per_sample = get_sorted_counts_per_sample(biom_table)
mapping_file_tuple = (real_map_data, real_map_headers)
# calculate the available subjects at each rarefaction level
results = make_selectors(sorted_counts_per_sample, min_seqs_sample,\
mapping_file_tuple, subject_category, verbose=verbose)
# save the output
fout = open(cleaned_fp,'w')
fout.write('#Sequences\tSubjects\tSamples\tMetadata\n')
fout.write('\n'.join(results))
fout.close()
def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
otu_table_fp = opts.otu_table_fp
output_dir = opts.output_dir
mapping_fp = opts.mapping_fp
tree_fp = opts.tree_fp
verbose = opts.verbose
print_only = opts.print_only
seqs_per_sample = int(opts.seqs_per_sample)
parallel = opts.parallel
min_seqs_sample = opts.min_seqs_sample
subject_category = opts.subject_name
try:
makedirs(output_dir)
except OSError:
if opts.force:
pass
else:
# Since the analysis can take quite a while, I put this check
# in to help users avoid overwriting previous output.
option_parser.error("Output directory already exists. Please choose"
" a different directory, or force overwrite with -f.")
## ******************** make_evident_selectors ********************
## The code for make_evident_selectors.py is here and has to go before the params
## validation as we need to know the main cats before creating the params file
map_data, headers, comments = parse_mapping_file(open(mapping_fp, 'U'))
biom_table = parse_biom_table(open(otu_table_fp, 'U'))
# getting valid samples from biom file
real_map_headers, real_map_data = filter_mapping_file(map_data, headers,\
biom_table.SampleIds, include_repeat_cols=False)
if subject_category not in real_map_headers:
option_parser.error('This column: %s is not in the mapping file, try %s'%\
(subject_category, real_map_headers))
sorted_counts_per_sample = get_sorted_counts_per_sample(biom_table)
mapping_file_tuple = (real_map_data, real_map_headers)
# calculate the available subjects at each rarefaction level
results, main_map_cat = make_selectors(sorted_counts_per_sample, min_seqs_sample,\
mapping_file_tuple, subject_category, verbose=verbose)
fout = open(join(output_dir,'selectors.txt'),'w')
fout.write('#Sequences\tSubjects\tSamples\tMetadata\n')
fout.write('\n'.join(results))
fout.close()
fout = open(join(output_dir,'mapping_file.txt'),'w')
fout.write(format_mapping_file(real_map_headers, real_map_data))
fout.close()
## ******************** make_evident_selectors ********************
fout = open(join(output_dir,'study_preferences.txt'),'w')
fout.write('%d\n' % seqs_per_sample)
fout.write('%s\n' % subject_category)
fout.close()
## ******************** filter_samples_from_otu_table ********************
## Filtering original biom file to only have samples above the max length to avoid
## ugly plots
alpha_biom_file = join(output_dir,'filtered_otu_table_for_alpha.biom')
fout = open(alpha_biom_file,'w')
sample_ids_to_keep = biom_table.SampleIds
filtered_otu_table = filter_samples_from_otu_table(biom_table,
sample_ids_to_keep,
min_count=seqs_per_sample,
max_count=inf)
fout.write(format_biom_table(filtered_otu_table))
fout.close()
## ******************** filter_samples_from_otu_table ********************
if opts.parameter_fp:
try:
parameter_f = open(opts.parameter_fp, 'U')
except IOError:
option_parser.error("Can't open parameters file (%s). Does it exist? " \
"Do you have read access?" % opts.parameter_fp)
params = parse_qiime_parameters(parameter_f)
parameter_f.close()
else:
params = parse_qiime_parameters(
['beta_diversity:metrics unweighted_unifrac',\
'make_rarefaction_plots:prefs_path %s' % join(output_dir,'prefs.txt'),
'make_rarefaction_plots:colorby %s' % ','.join(main_map_cat),
'make_rarefaction_plots:output_type memory',
'multiple_rarefactions:min %d' % int(seqs_per_sample/4),
'multiple_rarefactions:max %d' % (seqs_per_sample+1),
'multiple_rarefactions:step %d' % int(seqs_per_sample/4),
'multiple_rarefactions:num-reps 4',
])
# empty list returns empty defaultdict for now
jobs_to_start = opts.jobs_to_start
default_jobs_to_start = qiime_config['jobs_to_start']
validate_and_set_jobs_to_start(params,
jobs_to_start,
default_jobs_to_start,
parallel,
option_parser)
if print_only:
command_handler = print_commands
else:
command_handler = call_commands_serially
if verbose:
status_update_callback = print_to_stdout
else:
status_update_callback = no_status_updates
copyfile(otu_table_fp, join(output_dir,'raw.biom'))
run_beta_diversity_through_plots(otu_table_fp=otu_table_fp,
mapping_fp=mapping_fp,
output_dir=output_dir,
command_handler=command_handler,
params=params,
qiime_config=qiime_config,
color_by_interesting_fields_only=False,
sampling_depth=seqs_per_sample,
histogram_categories=None,
tree_fp=tree_fp,
parallel=parallel,
suppress_3d_plots=True,
suppress_2d_plots=True,
status_update_callback=status_update_callback)
output_dir = join(output_dir,'alpha')
run_alpha_rarefaction(otu_table_fp=alpha_biom_file,\
mapping_fp=mapping_fp,\
output_dir=output_dir,\
command_handler=command_handler,\
params=params,
qiime_config=qiime_config,\
tree_fp=tree_fp,\
num_steps=4,\
parallel=parallel,\
min_rare_depth=10,
max_rare_depth=20,
status_update_callback=status_update_callback,
plot_stderr_and_stddev=True)
