def serialize(self,population_size):
"""Print self out per ESTReMo's population serialization format"""
print population_size
for i in range(population_size):
print i
print len(self.motif)
for site in self.motif:
# TODO we should probably define the organism to
# include the ncr. For now, randomize the rest of the
# ncr
print site + random_site(self.ncr_size - len(site))
print 1 if type(self.recognizer) is SLP else 2
# TODO needs to be generalized to MLPs!
weights = concat(map(list,transpose(self.recognizer.input_layer)))
print len(weights)
for weight in weights:
print weight
import sys,os
print os.getcwd()
print sys.path
sys.path.append("data/estremo_motifs")
sys.path.append("src/generate_coevolved_motifs/estremo_files")
from Organism import Organism
print sys.path
from alpha_sweep_motifs import texts
from estremo_utils import random_site
orgs = map(lambda text:Organism(text,random_site(100000),overshooting=False),
texts)
motifs = [org.motif for org in orgs]
if __name__ == "__main__":
outfile = sys.argv[1]
motif_strings = map("\n".join,motifs)
with open(outfile,'w') as f:
f.write("\n\n".join(motif_strings))
