def _exec(p, request_dict): """execute a pristine analysis with""" p.set_analysis_type("rdp") p.threshold = request_dict.get('threshold') seperator = request_dict['seperator'] debug("storing seperator: '%s'" % seperator, p.files.log_file) open(p.files.seperator_file_path, 'w').write(seperator) 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 QA info", p.files.log_file) cmt = open(p.files.data_comment_file_path,'w') for line in open(p.files.data_file_path): if line.startswith(';'): cmt.write(line) cmt.close() #running rdp on data number_of_sequences = helper_functions.get_number_of_lines(p.files.data_file_path) / 2 debug("running rdp on %d sequences" % number_of_sequences, p.files.log_file) framework.tools.rdp.run_classifier(c.rdp_running_path, p.files.data_file_path, p.files.rdp_output_file_path, p.files.rdp_error_log_file_path) samples_dictionary(p) rdp_general_confidence_image(p) rdp_otu_confidence_analysis(p) rdp_samples_confidence_image(p) otu_library(p) rarefaction_curves(p) if hasattr(p,'threshold'): separate_low_confidence(p)