def sequences_bar_image(p):
samples_dict = DeserializeFromFile(p.files.samples_serialized_file_path)
debug("Generating number of sequences bar image", p.files.log_file)
samples = framework.tools.helper_functions.sorted_copy(samples_dict.keys())
framework.tools.bar.generate(
[(sample, samples_dict[sample]["tr"]) for sample in samples], p.images.samples_sequences_bar_path
)
def _append(p, request_dict):
# TODO: there should be one function in RDP that takes care of all these in one step.
# actually that one step solution should exist in every module that creates samples_dict eventually.
# so the mess here for new analyses and additional samples could be carried into their own modules.
# without putting everything together nicely in modules with standard hooks in them, there is no way to
# fix this mess.
p.threshold = request_dict.get('threshold')
if p.threshold:
debug("storing confidence threshold", p.files.log_file)
with open(p.files.threshold_path,'w') as f:
f.write(str(p.threshold))
debug("Extracting unique sample names from additional FASTA file", p.files.log_file)
additional_data_file_path = request_dict['additional_data_file_path']
seperator = open(p.files.seperator_file_path).read()
additional_samples = framework.tools.helper_functions.sorted_copy(framework.tools.rdp.extract_sample_names(additional_data_file_path, seperator))
original_samples = framework.tools.helper_functions.sorted_copy([sample.strip() for sample in open(p.files.all_unique_samples_file_path).readlines()])
number_of_sequences = sum(1 for l in open(additional_data_file_path) if l.startswith('>'))
additional_rdp_output_path = os.path.join(p.dirs.analysis_dir, "additional_rdp_output")
debug("Running rdp on %d additional sequences" % number_of_sequences, p.files.log_file)
framework.tools.rdp.run_classifier(c.rdp_running_path, additional_data_file_path, additional_rdp_output_path, p.files.rdp_error_log_file_path)
if p.threshold:
debug("Separating low confidence sequences", p.files.log_file)
lo_seqs = framework.tools.rdp.low_confidence_seqs(open(additional_data_file_path),
open(additional_rdp_output_path),
p.threshold,
seperator)
o = open(p.files.low_confidence_seqs_path,'a')
for s in lo_seqs:
o.write(s)
o.close()
#import pdb; pdb.set_trace()
debug("Merging additional data with the original RDP results", p.files.log_file)
framework.tools.rdp.merge(p.files.samples_serialized_file_path, additional_samples, original_samples, additional_rdp_output_path, p.files.rdp_output_file_path, seperator)
debug("Reading updated samples dict", p.files.log_file)
samples_dict = DeserializeFromFile(p.files.samples_serialized_file_path)
debug("Unique samples in samples dict being stored in samples file", p.files.log_file)
samples = framework.tools.helper_functions.sorted_copy(samples_dict.keys())
open(p.files.all_unique_samples_file_path, 'w').write('\n'.join(samples) + '\n')
rdp_general_confidence_image(p)
rdp_otu_confidence_analysis(p)
rdp_samples_confidence_image(p)
otu_library(p)
os.remove(additional_rdp_output_path)
def rdp_samples_confidence_image(p):
debug("Refreshing RDP Confidence per sample figure", p.files.log_file)
samples_dict = DeserializeFromFile(p.files.samples_serialized_file_path)
seperator = open(p.files.seperator_file_path).read()
samples = framework.tools.helper_functions.sorted_copy(samples_dict.keys())
framework.tools.rdp.sample_confidence_analysis(p.files.rdp_output_file_path, p.dirs.analysis_dir, seperator, samples)
def rdp_otu_confidence_analysis(p):
debug("Generating RDP confidence per otu figures", p.files.log_file)
samples_dict = DeserializeFromFile(p.files.samples_serialized_file_path)
samples = framework.tools.helper_functions.sorted_copy(samples_dict.keys())
seperator = open(p.files.seperator_file_path).read()
framework.tools.rdp.otu_confidence_analysis(p.files.rdp_output_file_path, p.dirs.type_specific_data_dir, seperator, samples)
