tview.py 文件源码

def __init__(self, bam:str, reference:str, columns:int=20000, cache:int=None, minor_gaps:bool=False):
        """Interface to samtools tview functionality.

        :param bam: path to bam file of reads aligned to a common
            reference.
        :param reference: path to fasta file of reference to which reads
            are aligned.
        :param columns: default number of tview columns to read in one go.
        :param cache: Currently not implemented.
        :param minor_gaps: encoded gaps in non-reference positions distinctly.
        """
        self.logger = logging.getLogger('TView')
        self._bam = bam
        self._reference = reference
        self._columns = columns
        self._cache = cache
        self._minor_gaps = minor_gaps
        if self._minor_gaps:
            raise NotImplementedError
        self._columns_per_base = 3 # reasonable estimate
        self._column_pad = 1.1 # multiplier when _columns_per_base is updated

        # crosscheck the inputs
        with pysam.AlignmentFile(bam, 'rb') as b:
            brefs = b.references
            blens = b.lengths
        rrefs = set(pysam.FastaFile(reference).references)
        sbrefs = set(brefs)
        if not sbrefs.issuperset(rrefs):
            raise ValueError("input bam and reference do not appear consistent: {} vs {}.".format(sbrefs, rrefs))
        self._refs = set(brefs)
        self._reflens = dict(zip(brefs, blens))

        self._pileup = None # buffered `Pileup` object