class WiggleCorrelator(object):
def __init__(self):
self._wiggle_parser = WiggleParser()
def correlate(self, wiggle_file_1, wiggle_file_2):
self._chrom_and_pos_value_pairs = {}
print("Replicon: Pearson correlation coefficient (p-value)")
for entry_1, entry_2 in zip(
self._wiggle_parser.entries(wiggle_file_1),
self._wiggle_parser.entries(wiggle_file_2)):
assert(entry_1.replicon == entry_2.replicon)
pos_value_pairs_1 = dict(entry_1.pos_value_pairs)
pos_value_pairs_2 = dict(entry_2.pos_value_pairs)
if len(pos_value_pairs_1) == 0 or len(pos_value_pairs_2) == 0:
print("%s: At least one replicon has no coverage for "
"this libs." % (entry_2.replicon))
continue
non_redu_pos = set(
pos_value_pairs_1.keys() + pos_value_pairs_2.keys())
values_1 = np.array(
[pos_value_pairs_1.get(pos, 0.0) for pos in non_redu_pos])
values_2 = np.array(
[pos_value_pairs_2.get(pos, 0.0) for pos in non_redu_pos])
pearson, pvalue = stats.pearsonr(values_1, values_2)
print("%s: %s (%s)" % (entry_1.replicon, pearson, pvalue))
class WiggleCorrelator(object):
def __init__(self, args):
self._wiggle_parser = WiggleParser()
self._method = args.method
self._rep_dict = dict([rep.split(':') for rep in args.rep_sizes.strip().split(',')])
def correlate(self, wiggle_file_1a, wiggle_file_2a, wiggle_file_1b = None, wiggle_file_2b = None ):
print("Replicon: %s correlation coefficient (p-value)" % self._method)
for entry_1a, entry_2a, entry_1b, entry_2b in zip(
self._wiggle_parser.entries(wiggle_file_1a),
self._wiggle_parser.entries(wiggle_file_2a),
self._wiggle_parser.entries(wiggle_file_1b),
self._wiggle_parser.entries(wiggle_file_2b)):
assert(entry_1a.chrom_name == entry_2a.chrom_name == entry_1b.chrom_name == entry_2b.chrom_name)
pos_value_pairs_1a = dict(entry_1a.pos_value_pairs)
pos_value_pairs_2a = dict(entry_2a.pos_value_pairs)
pos_value_pairs_1b = dict(entry_1b.pos_value_pairs)
pos_value_pairs_2b = dict(entry_2b.pos_value_pairs)
if (len(pos_value_pairs_1a) == 0 and len(pos_value_pairs_1b) == 0) or (
len(pos_value_pairs_2a) == 0 and len(pos_value_pairs_2b) == 0):
print("%s: At least one replicon has no coverage for "
"this libs." % (entry_1a.chrom_name))
continue
values_1 = np.array(
[pos_value_pairs_1a.get(pos, 0.0) for pos in range(1, int(self._rep_dict[entry_1a.chrom_name])+1)] +
[pos_value_pairs_1b.get(pos, 0.0) for pos in range(1, int(self._rep_dict[entry_1b.chrom_name])+1)])
values_2 = np.array(
[pos_value_pairs_2a.get(pos, 0.0) for pos in range(1, int(self._rep_dict[entry_2a.chrom_name])+1)] +
[pos_value_pairs_2b.get(pos, 0.0) for pos in range(1, int(self._rep_dict[entry_2b.chrom_name])+1)])
if self._method == "pearson":
corr, pvalue = stats.pearsonr(values_1, values_2)
else:
corr, pvalue = stats.spearmanr(values_1, values_2)
print("%s: %s (%s)" % (entry_1a.chrom_name, corr, pvalue))
def __init__(self):
self._wiggle_parser = WiggleParser()
def __init__(self, args):
self._wiggle_parser = WiggleParser()
self._method = args.method
self._rep_dict = dict([rep.split(':') for rep in args.rep_sizes.strip().split(',')])