def __call__(self, fasta):
"Run the method."
start_time = time.time()
ensure_dir_exists(self.options.output_dir)
predictions = []
# run MEME
self.meme_cmd_args, self.stdoutdata, self.starts, self.Zs, self.thetas, self.lambdas = run_meme(
fasta, self.options)
# parse output
from Bio import Motif
for motif in Motif.parse(open(os.path.join(self.options.output_dir, 'meme.txt')), "MEME"):
for instance in motif.instances:
# MEME parser seems to count from 1, not 0
start = instance.start - 1
prediction = instance.sequence_name, Interval(
start, start + motif.length), instance.strand == '-'
predictions.append(prediction)
logger.info('MEME took %.1f seconds', time.time() - start_time)
return predictions
def parse_meme_output_for_sites(meme_output):
"Parse MEME-like output"
logging.info('Parsing predictions from %s', meme_output)
predicted_sites = defaultdict(P.IntIntervalSet)
motifs = list(Motif.parse(open(meme_output), "MEME"))
for motif in motifs:
for instance in motif.instances:
logging.info('Prediction: sequence = %s; site = %s; pos = %3d',
instance.sequence_name, instance, instance.start)
predicted_sites[instance.sequence_name].add(
P.IntInterval(instance.start, instance.start + len(instance)))
return predicted_sites
options = stempy.get_default_options()
options.output_dir = os.path.join('output', 'test-meme-like-output')
options.min_w = options.max_w = 8
options.meme_like_output = 'meme.out'
algorithm = stempy.Algorithm(options)
fasta = os.path.join(os.path.dirname(__file__), 'fasta', 'T00759-tiny.fa')
algorithm(fasta)
logging.info('Showing MEME output from %s', algorithm.meme_like_output_file)
os.system('cat %s' % algorithm.meme_like_output_file)
#
# Test BioPython parser
#
from Bio import Motif
motifs = list(Motif.parse(open(algorithm.meme_like_output_file), "MEME"))
#
# Doesn't quite work with pycogent yet. Pycogent expects a summary section
# that contains sites in all the sequences
#
#from cogent import LoadSeqs
#from cogent.parse.meme import MemeParser
#results = MemeParser(open(algorithm.meme_like_output_file, 'U'))
#seqs = LoadSeqs(fasta, aligned=False)
#results.Alignment = seqs
#for motif in results.Motifs:
# module = motif.Modules[0]
# print module.ID, module.Evalue, len(module.NamedSeqs)
#
