def get_round(dct,rnd):
x = FindAllFiles()
set9 = x.query_dirname(rnd,-2,dct)
print 'files entered:',len(dct.keys())
print 'files returned, round %s:' % rnd,len(set9.keys())
set9 = x.sort_dirname(-1,set9)
return set9
def get_bydata(dct, data_name):
print 'files entered:', len(dct.keys())
x = FindAllFiles()
print data_name
set9 = x.query_dirname(data_name, -2, dct)
lst = set9.keys()
return sorted(lst)
def get_doz(dct, data_name):
print 'files entered:', len(dct.keys())
x = FindAllFiles()
print data_name
set9 = x.query_dirname(data_name, -2, dct)
set9 = x.sort_dirname(-2, set9)
# lst = set9.keys()
# return sorted(lst)
# return lst
return set9
def load_dct(cwd=my_dir,pattern='*.dat'):
# FindAllFiles
print('cwd:',cwd)
print('pattern:',pattern)
dct_find = {'cwd':cwd,'pattern':pattern}
x = FindAllFiles(dct_find)
x.get_files()
dct9 = x.sort_dirname(-1,x.dct)
print(len(dct9.keys()),'of',x.total)
return dct9
def load_dct(cwd=my_dir, pattern='*.dat'):
# FindAllFiles
print 'cwd:', cwd
print 'pattern:', pattern
dct_find = {'cwd': cwd, 'pattern': pattern}
x = FindAllFiles(dct_find)
# print x.pattern
x.get_files()
# x.print_query(x.dct)
print len(x.dct.keys()), 'of', x.total
set9 = x.dct
# x.dct (last pos.)
# set9 = x.sort_dirname(-1,x.dct)
# x.print_ [query,class]
# x.query_ [dirname,file,filename](searchstring,pos,dct)
# x.remove_[dirname,file,filename](searchstring,pos,dct)
# x.print_query(set9)
# print len(set9.keys()),'of',x.total
# sys.exit()
# return set9
set9 = x.remove_dirname('fail', None, set9)
set9 = x.remove_dirname('builder', None, set9)
set9 = x.remove_filename('_new.dat', set9)
set9 = x.remove_filename('_bac.dat', set9)
set9 = x.remove_dirname('dat', -1, set9)
print len(set9.keys()), 'of', x.total
set9 = x.sort_dirname(-1, set9)
return set9
def get_round(dct, round_name):
print 'files entered:', len(dct.keys())
x = FindAllFiles()
print round_name
set9 = x.query_dirname(round_name, -3, dct)
if len(set9.keys()) == 0:
set9 = x.query_dirname(round_name, -4, dct)
# if ((round_name == 'round_16') and (len(set9.keys()) == 0)):
# set9 = x.query_dirname(round_name,-4,dct)
set9 = x.sort_dirname(-1, set9)
print 'file returned:', len(set9.keys())
return set9
def load_dct(cwd=my_dir, pattern='*.dat'):
# FindAllFiles
print 'cwd:', cwd
print 'pattern:', pattern
dct_find = {'cwd': cwd, 'pattern': pattern}
x = FindAllFiles(dct_find)
# print x.pattern
x.get_files()
# x.print_query(x.dct)
# print len(x.dct.keys()),'of',x.total
set9 = x.remove_dirname('fail', None, x.dct)
set9 = x.remove_dirname('example', None, set9)
set9 = x.remove_dirname('tops_extra', None, set9)
set9 = x.query_dirname("round_%d" % rnd, None, set9)
set9 = x.sort_dirname(-1, set9)
return set9
def load_dct(cwd=my_dir,pattern='*_top.dat'):
# FindAllFiles
print 'cwd:',cwd
print 'pattern:',pattern
dct_find = {'cwd':cwd,'pattern':pattern}
x = FindAllFiles(dct_find)
x.get_files()
# x.print_ [query,class]
# x.query_ [dirname,file,filename](searchstring,pos,dct)
# x.remove_[dirname,file,filename](searchstring,pos,dct)
set9 = x.remove_dirname('fail',None,x.dct)
set9 = x.remove_dirname('example',None,set9)
set9 = x.remove_dirname('tops_extra',None,set9)
set9 = x.query_dirname("round_%d" % proj_round,None,set9)
set9 = x.sort_dirname(-1,set9)
return set9
def load_dct(cwd=my_dir,pattern='*.dat'):
# FindAllFiles
print 'cwd:',cwd
print 'pattern:',pattern
dct_find = {'cwd':cwd,'pattern':pattern}
x = FindAllFiles(dct_find)
x.get_files()
# print len(x.dct.keys()),'of',x.total
set9 = x.remove_dirname('fail',None,x.dct)
set9 = x.remove_dirname('example',None,set9)
set9 = x.remove_dirname('tops_extra',None,set9)
# if((rnd == '10') or (rnd == '11')):
# set9 = x.remove_dirname('_nop_',None,set9)
# set9 = x.remove_dirname('_rev_',None,set9)
set9 = x.query_dirname("round_%d" % rnd,None,set9)
set9 = x.sort_dirname(-1,set9)
# x.print_query(set9)
# sys.exit()
print 'dct_matches:',len(set9.keys())
return set9
def load_dct(cwd=my_dir, pattern='*.dat'):
# FindAllFiles
print 'cwd:', cwd
print 'pattern:', pattern
dct_find = {'cwd': cwd, 'pattern': pattern}
x = FindAllFiles(dct_find)
# print x.pattern
x.get_files()
# x.print_query(x.dct)
print len(x.dct.keys()), 'of', x.total
set9 = x.remove_dirname('fail', None, x.dct)
# set9 = x.query_filename(rnd,set9)
set9 = x.sort_filename(set9)
lst = []
for k, v in set9.items():
lst.append(v['file'])
return lst
def check_hsa_analysis(dct):
for i,k in enumerate(dct.keys()):
os.chdir(dct[k]['dirname'])
# FindAllFiles
dct_hsa = {'cwd':dct[k]['dirname'],'pattern':'*.dat'}
H = FindAllFiles(dct_hsa)
set9 = H.get_files()
# H.query_ [dirname,file,filename](searchstring,pos,dct)
# H.remove_[dirname,file,filename](searchstring,pos,dct)
set9 = H.query_file('hsa',set9)
set9 = H.sort_dirname(-1,set9)
H.print_query(set9)
# set9
print(len(set9.keys()),'of',H.total)
# if ((not os.path.exists('hsa_current')) and (len(set9.keys()) != 0)):
# if (not os.path.exists('hsa_%s' % new_dir)):
if ((dct[traj]['dirname'] == dct[k]['dirname']) and (not os.path.exists('hsa_current'))):
print('making hsa_current')
os.makedirs('hsa_current')
# hcount = 0
for h in set9.keys():
# print h
if os.path.basename(set9[h]['dirname']) == os.path.basename(dct[k]['dirname']):
new_hsa_cur = os.path.join(dct[k]['dirname'],'hsa_current',set9[h]['filename'])
# print 'moving to hsa_current:',new_hsa_cur
# hcount += 1
os.rename(set9[h]['file'],new_hsa_cur)
lst_hsa = glob.glob('hsa_current/hsa*.dat') # 1
if len(lst_hsa) > 0:
print('base:',os.path.basename(dct[k]['dirname']))
print(lst_hsa)
def sort_routine1(dct):
x = FindAllFiles()
print 'files entered:', len(dct.keys())
def get_retraction_dct(dct):
set9 = dct
print len(set9.keys())
x = FindAllFiles()
if rnd == 16:
set_nop = x.remove_dirname("_nop_00",None,set9)
else:
set_nop = x.query_dirname("_nop_",None,set9)
set_rev = x.query_dirname("_rev_",None,set9)
set10 = x.merge_dct([set_rev,set_nop])
# print "Lengths:"
# print len(set_rev.keys())
# print len(set_nop.keys())
# print len(set10.keys())
# sys.exit()
if rnd == 16:
set_for = x.query_dirname("_nop_00",None,set9)
else:
set_for = x.remove_dirname("_rev_",None,set9)
set_for = x.remove_dirname("_nop_",None,set_for)
# print "Forwards:"
# print len(set_for.keys())
# sys.exit()
# lst_forward_names = []
# for k,v in set10.iteritems():
# # print k,v['dirname'].split('/')[-1]
# # print v
# proj_name = v['dirname'].split('/')[-1]
# forwards = proj_name.split('_nop_')[0]
# lst_forward_names.append(forwards)
lst_tup_for_retract = []
# print set_for.keys()
# print set10.keys()
for k,v in set_for.iteritems():
# print k,v['name']
for k1,v1 in set10.iteritems():
if rnd == 16:
name_ser = v['name'].split('_nop_')[0]
if re.search(name_ser,v1['name']) != None:
# print v['name'],v1['name']
# print (k,k1)
lst_tup_for_retract.append((k,k1))
else:
if re.search(v['name'],v1['name']) != None:
# print v['name'],v1['name']
# print (k,k1)
lst_tup_for_retract.append((k,k1))
# for name in lst_forward_names:
# # print name
# for k,v in set_for.iteritems():
# if re.search(name,v['dirname']) != None:
# # print k,name
# f1 = k
# break
# try:
# print f1
# except:
# continue
# for k,v in set10.iteritems():
# if re.search(name,v['dirname']) != None:
# if (f1,k) not in lst_tup_for_retract:
# lst_tup_for_retract.append((f1,k))
# break
# for tup in lst_tup_for_retract:
# print tup
# pass
print "retractions:",len(lst_tup_for_retract)
# sys.exit()
return lst_tup_for_retract
plot_type = 'fe' # fe | tension | rmsd | rdf
data_name = dataname # seed #
# save_fig(0,'fig','%s_%s_%s' % (result_type,plot_type,data_name))
combined_name = '%s_%s_%s' % (result_type, plot_type, data_name)
# --------------------------------------------------------- #
# Import Data! (3/4) #
# --------------------------------------------------------- #
# mylib
my_library = os.path.expanduser('~/.pylib')
sys.path.append(my_library)
from mylib.FindAllFiles import *
# FindAllFiles
dct_find = {'cwd': my_dir, 'pattern': '.dat'}
x = FindAllFiles(dct_find)
x.get_files()
set9 = x.dct
# x.print_query(set9)
set9 = x.remove_filename('curvature', set9)
set9 = x.remove_filename('distance_proto_', set9)
set9 = x.remove_dirname('fail', -2, set9)
set9 = x.remove_filename('LOG', set9)
set9 = x.remove_filename('contact', set9)
set9 = x.remove_filename('mt_angles', set9)
set9 = x.remove_filename('indices', set9)
set9 = x.remove_filename('tubulin_inter', set9)
# x.print_query(set9)
set9 = x.query_dirname('3kinesin13', -3, set9)
# set9 = x.sort_dirname(-2,set9)
# x.print_query(set9)
if args['unit'] == None:
unit = 'dimer'
else:
unit = args['unit']
# --------------------------------------------------------- #
# Import Data! (3/4) #
# --------------------------------------------------------- #
# mylib
my_library = os.path.expanduser('~/.pylib')
sys.path.append(my_library)
from mylib.FindAllFiles import *
# FindAllFiles
dct_find = {'cwd': my_dir, 'pattern': '.dat'}
x = FindAllFiles(dct_find)
x.get_files()
print len(x.dct.keys()), 'of', x.total
set9 = x.remove_dirname('fail', -2, x.dct)
set9 = x.query_file('curvature_local', set9)
set9 = x.sort_dirname(-2, set9)
print len(set9.keys()), 'of', x.total
# sys.exit()
# data_name
set9 = x.query_dirname(str(data_name), -2, set9)
set9 = x.sort_dirname(-1, set9)
x.print_query(set9)
print len(set9.keys()), 'of', x.total
# trajectory
if args['unit'] == None:
unit = 'dimer'
else:
unit = args['unit']
# --------------------------------------------------------- #
# Import Data! (3/4) #
# --------------------------------------------------------- #
# mylib
my_library = os.path.expanduser('~/.pylib')
sys.path.append(my_library)
from mylib.FindAllFiles import *
# FindAllFiles
dct_find = {'cwd': my_dir, 'pattern': '.dat'}
x = FindAllFiles(dct_find)
x.get_files()
set9 = x.dct
# x.dct (last pos.)
# x.sort_dirname
# x.print_query,_class
# x.query_ [dirname,file,filename](searchstring,pos,dct)
# x.remove_[dirname,file,filename](searchstring,pos,dct)
set9 = x.remove_dirname('fail', -2, set9)
set9 = x.query_filename('distance_proto_centroids', set9)
# x.print_query(set9)
print len(set9.keys()), 'of', x.total
set9 = x.query_dirname(str(data_name), -2, set9)
set9 = x.sort_dirname(-2, set9)
x.print_query(set9)
print len(set9.keys()), 'of', x.total
def load_angle_dct(cwd=my_dir, pattern='*.dat'):
# FindAllFiles
print 'cwd:', cwd
print 'pattern:', pattern
dct_find = {'cwd': cwd, 'pattern': pattern}
x = FindAllFiles(dct_find)
# print x.pattern
x.get_files()
# x.print_query(x.dct)
print "Grand total:", len(x.dct.keys()), 'of', x.total
# x.dct (last pos.)
# set9 = x.sort_dirname(-1,x.dct)
# x.print_ [query,class]
# x.query_ [dirname,file,filename](searchstring,pos,dct)
lst_dct = []
print "Rounds:", rnd
# if rnd == None:
# rnd = []
if rnd != None:
for r in rnd:
set9 = x.query_dirname("round_%s" % r, None, x.dct)
lst_dct.append(set9)
# x.print_query(set9)
print "subtotal:", len(set9.keys()), 'of', x.total
# print len(set9.keys())
set7 = x.merge_dct(lst_dct)
# x.print_query(set7)
print "subtotals:", len(set7.keys()), 'of', x.total
lst_dct = []
print "Positions:", position
# if position == None:
# position = []
if position != None:
for p in position:
set9 = x.query_dirname(p, -1, x.dct)
lst_dct.append(set9)
# x.print_query(set9)
print "subtotal:", len(set9.keys()), 'of', x.total
# print len(set9.keys())
set8 = x.merge_dct(lst_dct)
# x.print_query(set8)
print "subtotals:", len(set8.keys()), 'of', x.total
if ((rnd != None) and (position != None)):
set9 = x.get_overlapping_entries(set7, set8)
elif (rnd != None):
set9 = set7
elif (position != None):
set9 = set8
else:
set9 = x.dct
print "Overlaps:", len(set9.keys()), 'of', x.total
# x.remove_[dirname,file,filename](searchstring,pos,dct)
# x.print_query(set9)
# x.print_query(set9)
# sys.exit()
return set9
# evenodd = args['evenodd']
# ./plot_proto_angles_from3centroid.py -n 10 -d 123
# ./plot_proto_angles_from3centroid.py -d 123 -x 0 [1,2,3]
# ./plot_tubulin_angles.py -d 123 -t 1 -e 2
if line_size == None: # 10
line_size = 10
# --------------------------------------------------------- #
# Import Data! (3/4) #
# --------------------------------------------------------- #
# FindAllFiles
dct_find = {'cwd': my_dir, 'pattern': 'dat'}
x = FindAllFiles(dct_find)
x.get_files()
# x.print_query(x.dct)
set9 = x.dct
print len(x.dct.keys()), 'of', x.total
# sys.exit()
# x.dct (last pos.)
# x.sort_dirname
# x.print_query,_class
# x.query_ [dirname,file,filename](searchstring,pos,dct)
# x.remove_[dirname,file,filename](searchstring,pos,dct)
set9 = x.query_dirname('3kinesin', -3)
set9 = x.query_filename('tubulin', set9)
set9 = x.remove_dirname('fail', -2, set9)
set9 = x.remove_dirname('contact_maps', -1, set9)
set9 = x.sort_dirname(-2, set9)
