def run_meme_on_start(fasta, seed, num_sites, score, options):
import stempy.meme as meme
_meme_cmd_args, stdoutdata, starts, _Zs, _thetas, _lambdas = meme.run_meme(fasta, options, extra_args=(
'-nsites', str(num_sites), '-cons', seed, '-w', str(len(seed)))
)
if 1 != len(starts):
raise RuntimeError(
'Expecting only one start from MEME:\n%s' % stdoutdata)
return starts[0]
Code to run the MEME EM algorithm.
"""
import logging
from cookbook.script_basics import setup_logging
setup_logging(__file__, level=logging.INFO)
import stempy
import stempy.meme as meme
import sys
#
# parse options
#
options, args = stempy.parse_options(stempy.add_options)
if len(args) != 3:
raise RuntimeError('USAGE: %s <options> fasta seed num_sites', sys.argv[0])
fasta = args.pop(0)
seed = args.pop(0)
num_sites = int(args.pop(0))
meme_cmd_args, stdoutdata, starts, Zs = meme.run_meme(
fasta,
options,
extra_args=(
'-nsites', str(num_sites), '-cons', seed, '-w', str(
len(seed)), "-print_z"
)
)