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)