iCLIP.counting.count_intervals¶

iCLIP.counting.count_intervals(getter, intervals, contig, strand='.', dtype='uint32', use_centre=False, get_all_and_mask=True)¶

Count the crosslinked bases across a set of intervals

Parameters:	getter (_getter function or pysam.AlignmentFile) – The getter function to retrieve the cross-links from. Returned from make_getter. intervals* (iter of tuples) – The intervals to retrieve cross-links from as an iterable of (start, end) tuples. contig (str) – strand ({"+", "-", "."}) – If “.” then the sum of counts on both strands is returned. dtype (str) – numpy dtype used for storing counts. Larger dtypes reduce chance of overflow, but use more memory. Defaults to ‘uint32’. get_all_and_mask (bool, optional) – Instead of fetching each exon indevidually from the getter, fetch entire chromsome region, and then subset to things in the interval.
Returns:	Series of integer counts, where the index of the Series is the genome coordinates. Series is spares (i.e. 0 count bases are excluded)
Return type:	pandas.Series