def analysis(saveto_h5, max_num_dataset=10):
""" A bad way to organize a sequence of analysis """
# h5 files to read, tables, and paths to tables are encoded inside the analysis
# ideally they would be refactored into a configuration file
polar_h5 = tables.openFile('GA4_mon_polar_analysis.h5', mode='a')
nonpolar_h5 = tables.openFile('GA4_mon_nonpolar_analysis.h5', mode='a')
# analyze and aggregate all data for each iso and store each in a separate table
for system in ["mon"]:
for iso in ["scyllo", "chiro"]:
# clear the results
analysis_results = []
for i in range(0, max_num_dataset):
table_path = '/%(system)s/%(iso)s%(i)d' % vars()
print "analyzing", table_path
polar_table = myh5.getTable(polar_h5, table_path)
nonpolar_table = myh5.getTable(nonpolar_h5, table_path)
if polar_table != None and nonpolar_table != None:
polar_array = utils.convert_to_numpy(polar_table)
nonpolar_array = utils.convert_to_numpy(nonpolar_table)
s = stoichiometry(polar_array[0:5001, 1:], nonpolar_array[0:5001,1:])
analysis_results.append(s)
myh5.save(saveto_h5, numpy.vstack(analysis_results), "/mon_analysis/stoichiometry_%(iso)s" % vars())
def mon(offset=0, max_num_dataset=10):
"""This is computes the intersection of polar and nonpolar binding of inositol"""
polar_h5 = tables.openFile('GA4_mon_polar_analysis.h5', mode='a')
nonpolar_h5 = tables.openFile('GA4_mon_nonpolar_analysis.h5', mode='a')
# print >>f, "#table_name polar nonpolar p_and_np polar_fraction nonpolar_fraction p_and_np_fraction total_inositols bound unbound K"
for system in ["mon"]:
for iso in ["scyllo", "chiro"]:
data = []
errorlist = []
for i in range(0, max_num_dataset):
table_path = '/%(system)s/%(iso)s%(i)d' % vars()
print "analyzing",table_path
polar_table = myh5.getTable(polar_h5, table_path)
nonpolar_table = myh5.getTable(nonpolar_h5, table_path)
if polar_table != None and nonpolar_table != None:
polar_array = utils.convert_to_numpy(polar_table)
nonpolar_array = utils.convert_to_numpy(nonpolar_table)
print "computing intersection ..."
polar, nonpolar, p_and_np, total_inositol = intersect(polar_array[0:5001,1:], nonpolar_array[0:5001,1:])
print "computing binding constant ..."
bound,unbound = binding(polar_array[offset:5001, 1:], nonpolar_array[offset:5001, 1:])
# errorlist.append(binding_error(polar_array[offset:5001, 1:], nonpolar_array[offset:5001, 1:], block_size=1000))
total = float(polar + nonpolar + p_and_np)
# print >>f, table_path, polar, nonpolar, p_and_np, polar/total, nonpolar/total, p_and_np/total, total_inositol, bound, unbound, unbound/float(bound)*125
data.append(numpy.array([polar, nonpolar, p_and_np, total, total_inositol, bound, unbound]))
else:
print "table not found"
data = numpy.vstack(data)
# numpy.savetxt('%(iso)s_data.txt' % vars(), data, fmt='%-0.3f')
data_sum = numpy.sum(data, axis=0)
# nasty output
heading = ["polar", "nonpolar", "p_and_np", "total", "total_inositol", "nbound", "nunbound"]
d = dict(zip(heading, data_sum))
f = open('%(iso)s_data_aggregation.txt' % vars(), 'w')
for key in sorted(d.keys()):
print >>f, key, d[key]
f.close()
#compute error
blocklist = block_average(data)
numpy.savetxt('%(iso)s_blocks.txt' % vars(), blocklist, fmt='%.3f')
def disordered():
"""This is computes the intersection of polar and nonpolar binding of inositol"""
polar_h5 = tables.openFile('GA4_disordered_polar_analysis.h5', mode='a')
nonpolar_h5 = tables.openFile('GA4_disordered_nonpolar_analysis.h5', mode='a')
f = open('data.txt', 'w')
print >>f, "#table_name polar nonpolar p_and_np polar_fraction nonpolar_fraction p_and_np_fraction total_inositols nframes bound unbound Kd"
for system in ["ap1f", "oct"]:
for iso in ["scyllo", "chiro"]:
for i in range(0,6):
table_path = '/%(system)s/%(iso)s%(i)d' % vars()
polar_table = myh5.getTable(polar_h5, table_path)
nonpolar_table = myh5.getTable(nonpolar_h5, table_path)
if polar_table != None and nonpolar_table != None:
# Note need to specify float64, since now pytables is all 32 bit
polar_array = utils.convert_to_numpy(polar_table, dtype=numpy.float64)
nonpolar_array = utils.convert_to_numpy(nonpolar_table, dtype=numpy.float64)
# need to exclude first column of nonpolar data because its time
polar,nonpolar,p_and_np, total_inositol = intersect(polar_array, nonpolar_array[:,1:])
bound,unbound = binding(polar_array, nonpolar_array[:,1:])
total = float(polar + nonpolar + p_and_np)
print >>f, table_path, polar, nonpolar, p_and_np, polar/total, nonpolar/total, p_and_np/total, total_inositol, total_inositol/2, bound, unbound, unbound/float(bound)*123
