def update_rcParams():
font_path = util.slash(
os.getenv('HOME')) + '.fonts/adobe/Adobe_Caslon_Pro_Regular.ttf'
prop = font_manager.FontProperties(fname=font_path)
rcParams['font.family'] = prop.get_name()
#rcParams['font.family'] = 'Adobe Caslon Pro' # cursive, http://matplotlib.org/examples/pylab_examples/fonts_demo.html
rcParams[
'font.serif'] = 'Helvetica' #['Bitstream Vera Sans', 'DejaVu Sans', 'Lucida Grande', 'Verdana', 'Geneva', 'Lucid', 'Arial', 'Helvetica', 'Avant Garde', 'sans-serif']
rcParams['axes.labelsize'] = 16
rcParams['axes.titlesize'] = 20
rcParams['grid.alpha'] = 0.1
rcParams['axes.grid'] = True
rcParams['savefig.pad_inches'] = .001
rcParams['grid.color'] = 'grey'
rcParams[
'xtick.color'] = 'black' # ax.tick_params(axis='x', colors='red'). This will set both the tick and ticklabel to this color. To change labels' color, use: for t in ax.xaxis.get_ticklabels(): t.set_color('red')
rcParams[
'xtick.direction'] = 'out' # ax.get_yaxis().set_tick_params(which='both', direction='out')
rcParams['xtick.labelsize'] = 12
rcParams['xtick.major.pad'] = 1.0
rcParams['xtick.major.size'] = 6 # how long the tick is
rcParams['xtick.major.width'] = 1
rcParams['xtick.minor.pad'] = 1.0
rcParams['xtick.minor.size'] = 2.5
rcParams['xtick.minor.width'] = 0.5
rcParams['xtick.minor.visible'] = False
rcParams['ytick.color'] = 'black' # ax.tick_params(axis='x', colors='red')
rcParams[
'ytick.direction'] = 'out' # ax.get_xaxis().set_tick_params(which='both', direction='out')
rcParams['ytick.labelsize'] = 12
rcParams['ytick.major.pad'] = 2
rcParams['ytick.major.size'] = 6
rcParams['ytick.major.width'] = 1
rcParams['ytick.minor.pad'] = 2.0
rcParams['ytick.minor.size'] = 2.5
rcParams['ytick.minor.width'] = 0.5
rcParams['ytick.minor.visible'] = False
return prop
import os, sys
sys.path.insert(0, os.getenv('lib'))
import utilv4 as util
for root, dirs, files in os.walk(sys.argv[1]):
for d in dirs:
for r2, ds2, fs2 in os.walk(os.path.join(root, d)):
CSVs = [
f.replace('_EXECSTATS', '') for f in fs2
if f.split('.')[-1] == 'csv'
]
if len(CSVs) > 1 and d == 'data_points':
# we may be in a data_points dir
# RN_Bacteria-RegulonDB_RAW_INSTANCES_p100.0_t050.0_V4NU_DPSOLVER_1X_BOTH_REVERSE_alpha0.2.June-18-2017-h17m49s43.csv
PTs = [(csv.split('_')[-8], csv.split('_')[-7])
for csv in CSVs]
for pt in set(PTs):
if PTs.count(pt) > 1:
#print ('\n'.join(CSVs))
#sys.exit(1)
print(
util.slash(os.path.join(root, d)) + '*' + pt[0] +
'_' + pt[1] + '*')
source, target = random.SystemRandom().choice(
M.edges()) # pick a random edge
M.remove_edge(source, target)
i = 0
while i < number_of_edges_to_swap:
source = random.SystemRandom().choice(
M.nodes()) # pick a random source
target = random.SystemRandom().choice(
M.nodes()) # pick a random target
sign = random.SystemRandom().choice(
['+', '-']) # do we wanna randomize the sign? yes
if (source, target) not in M.edges():
M.add_edge(source, target, sign=sign)
i += 1
savepath = util.slash('/'.join(
edge_file.split('/')[0:-1])) + 'RN_' + edge_file.split('/')[-1]
writer = open(savepath, 'w')
writer.write('source target sign')
for source, target in M.edges():
sign = str(M[source][target]['sign'])
if sign != '+' and sign != '-':
if int(sign) == 1:
sign = '+'
elif int(sign) == -1:
sign = '-'
else:
print("FATAL: I don't recognize this sign " + str(sign) +
'\nExiting....')
sys.exit(1)
break
Edges = []
for L in Leafs:
Edges += adjacents(M, L) # edges
Edges = list(set(Edges))
swap(M, Edges, Hubs, quite=quite)
writeout(M, savename)
########################################################
########################################################
if __name__ == '__main__':
networks = getCommandLineArgs()
analogs = zip([
util.slash('/'.join(n.split('/')[0:-1])) + 'NH_' + n.split('/')[-1]
for n in networks
], [
util.slash('/'.join(n.split('/')[0:-1])) + 'NL_' + n.split('/')[-1]
for n in networks
])
for (netpath, savename) in zip(networks, analogs):
M = init.load_network({
'network_file': netpath,
'biased': False
},
undirected=False,
quite=False)
stats = {'before': {}, 'after': {}}
crunch_stats(M, stats['before'])
import sys, os
sys.path.insert(0, os.getenv('lib'))
import init, utilv4 as util
sys.path.insert(0, util.slash(os.getenv('util'))+'collect_files_by_name_pattern')
import collector_by_ANDin_patterns as collect
########################################################################
def getCommandLineArgs():
if len(sys.argv) < 2:
sys.stdout.write ("Usage: python3 max_BD.py [/path/to/scratch/dir/]\nExiting..\n")
sys.exit()
return str(sys.argv[1])
########################################################################
def print_title(patterns,root_dir):
sys.stdout.write("\n inspecting csv files in "+str(root_dir)+" that meet the patterns "+str(patterns)+"\n")
sys.stdout.write("\n "+"="*70)
sys.stdout.write ("\n | "+"Network"+" "*7+" "*11+"configs"+" "*14+"max(B)".ljust(7,' ')+"max(D)".ljust(7,' ')+' |')
sys.stdout.write("\n "+"="*70)
sys.stdout.flush()
########################################################################
patterns = ['RAW','INSTANCES', 'p100.0', 't100.0', 'csv']
root_dir = getCommandLineArgs().strip()
MATCHES = collect.get_matches(patterns, root_dir)
print_title(patterns,root_dir)
#$scratches/IntAct/AN_IntAct/v4_alpha0.2/v4eb_minknap_4X_target_scramble/02_raw_instances_simulation/data_points/AN_IntAct_RAW_INSTANCES_p000.1_t005.0_V4EB_MINKNAP_4X_TARGET_SCRAMBLE_alpha0.2.November-08-2016-h06m07s37.csv
STAMPS = []
for file_path in MATCHES:
if not os.path.isfile(file_path):
sys.stdout.write ("\nnot a file, skipping: "+file_path)
continue