#
# Copyright John Reid 2011
#
"""
Matches predictions in MEME output format to details about planted sites in headers of fasta files.
"""
import logging
from stempy.planted_sites import parse_fasta_for_sites, parse_meme_output_for_sites, calculate_positives_and_negatives
from infpy.roc import RocCalculator
logging.basicConfig(level=logging.INFO)
if 3 != len(sys.argv):
raise RuntimeError('USAGE: %s <fasta> <meme-output>' % sys.argv[0])
fasta_file = sys.argv[1]
meme_output = sys.argv[2]
records, true_sites = parse_fasta_for_sites(fasta_file)
predicted_sites = parse_meme_output_for_sites(meme_output)
TP, TN, FN, FP = calculate_positives_and_negatives(
records, true_sites, predicted_sites)
roc = RocCalculator(TP, FP, TN, FN)
logging.info(roc)
options.min_w = 6
options.max_w = 11
options.output_dir = os.path.join('output', 'test-steme-accuracy', data_set)
meme_output = os.path.join(options.output_dir, options.meme_like_output)
#
# Run the STEME algorithm
#
algorithm = stempy.Algorithm(options)
algorithm(fasta_file)
#
# Analyse output
#
records, true_sites = parse_fasta_for_sites(fasta_file)
predicted_sites = parse_meme_output_for_sites(meme_output)
TP, TN, FN, FP = calculate_positives_and_negatives(records, true_sites, predicted_sites)
roc = RocCalculator(TP, FP, TN, FN)
rocs[data_set] = roc
#
# Run MEME as well if asked to
#
if cmd_line_options.run_meme:
from stempy import meme
options.output_dir = os.path.join(options.output_dir, 'MEME')
meme_algorithm = meme.Algorithm(options)
meme_algorithm(fasta_file)
#
# Analyse MEME output
