sys.path.append('/home/hudaiber/Projects/lib/BioPy/')
sys.path.append('/home/hudaiber/Projects/SystemFiles/')
import global_variables as gv
sys.path.append(gv.project_code_path)
from lib.db.archea import db_tools, neighborhoods_path
from lib.utils import tools as t
import os
target_profiles = t.target_profiles()
target_profiles = [l.strip() for l in open('/Volumes/pan1/patternquest/Projects/NewSystems/data/Archea/arCOG/selected_arcogs.txt').readlines()]
profile2def = t.map_profile2def()
gid2arcog_cdd = t.map_gid2arcog_cdd()
neighborhood_files_path = neighborhoods_path()
neighborhood_files_path = '/Volumes/pan1/patternquest/Projects/NewSystems/data/Archea/genes_and_flanks/win_10/pty/'
def write_to_xls(xls_file, kplets):
community = set()
[community.update(kplet.codes) for kplet in kplets]
_file2kplets = {}
for kplet in kplets:
for f in kplet.files:
if f in _file2kplets:
_file2kplets[f].append(kplet)
else:
# dump_file = bz2.BZ2File(os.path.join(save_path, 'pentaplets_merged_across.p.bz2'), 'w')
# pickle.dump(pentaplets, dump_file)
# dump_file = bz2.BZ2File(os.path.join(save_path, 'quadruplets_merged_across.p.bz2'), 'w')
# pickle.dump(quadruplets, dump_file)
# dump_file = bz2.BZ2File(os.path.join(save_path, 'triplets_merged_across.p.bz2'), 'w')
# pickle.dump(triplets, dump_file)
# dump_file = bz2.BZ2File(os.path.join(save_path, 'duplets_merged_across.p.bz2'), 'w')
# pickle.dump(duplets, dump_file)
if __name__ == '__main__':
print 'Pre-Loading dictionaries'
target_profiles = t.bacteria_target_profiles()
profile2def = t.map_cdd_profile2def()
gid2arcog_cdd = t.map_gid2arcog_cdd()
neighborhood_files_path = neighborhoods_path()
profile_id2code = map_id2cdd()
# for limit_to, report_dir in zip([300, 500, 1000, 100000],['top_300', 'top_500', 'top_1000', 'top_100000']):
#
# print "Limit_to:", limit_to
# print
# generate_plots(limit_to, report_dir, target_profiles, profile2def, gid2arcog_cdd, neighborhood_files_path, profile_id2code)
# print 'Done'
# print "------------------------"
data_path = os.path.join(gv.project_data_path, 'Bacteria/pickle/')
print 'Generating pickles'
for limit_to in [100000]: