--- a +++ b/singlecellmultiomics/statistic/trimming.py @@ -0,0 +1,27 @@ +#!/usr/bin/env python3 +# -*- coding: utf-8 -*- + +from .statistic import StatisticHistogram +import singlecellmultiomics.pyutils as pyutils + + +class TrimmingStats(StatisticHistogram): + def __init__(self, args): + StatisticHistogram.__init__(self, args) + self.totalFragmentsTrimmed = 0 + + def processRead(self, R1,R2=None): + + for read in [R1,R2]: + if read is None: + continue + + if read.has_tag('a1') or read.has_tag( + 'eB') or read.has_tag('A2') or read.has_tag('EB'): + self.totalFragmentsTrimmed += 1 + + def __repr__(self): + return f'Trimmed fragments: {self.totalFragmentsTrimmed}' + + def __iter__(self): + yield 'Trimmed fragments', self.totalFragmentsTrimmed