#!/usr/bin/env python3
# -*- coding: utf-8 -*-
import collections
import pandas as pd
import numpy as np
import singlecellmultiomics.pyutils as pyutils
[docs]class Statistic(object):
"""
Statistic object, initialised with arguments
Parameters
----------
args : argparse object
"""
def __init__(self, args):
self.args = args
[docs] def processRead(self, R1,R2=None):
"""
Update the statistic with information from READ
Parameters
----------
read : PySAM Aligned segment
Returns
----------
None
"""
pass
def __repr__(self):
return 'dummy'
[docs]class StatisticHistogram(Statistic):
def __init__(self, args):
Statistic.__init__(self, args)
self.histogram = collections.Counter()
def __repr__(self):
return f'Mean {pyutils.meanOfCounter(self.histogram)}, SD:{pyutils.varianceOfCounter(self.histogram)}'
def __iter__(self):
return iter(self.histogram.most_common())
[docs] def to_csv(self, path):
pd.DataFrame({__class__.__name__: self.histogram}).to_csv(path)