INNER CODE UNIT · Python

FastaIndex

Gabaldonlab/redundans · bin/FastaIndex.py:28

class FastaIndex(object):
    """Facilitate Fasta index (.fai) operations compatible
    with samtools faidx (http://www.htslib.org/doc/faidx.html).
    """
    def __init__(self, handle, verbose=0, log=sys.stderr):
        """ """
        ext = ".fai"
        self.verbose = verbose
        self.log = log.write
        self.genomeSize = 0
        self.whitespaces_in_headers = False
        # guess handle
        if type(handle) is str and os.path.isfile(handle): 
            handle = open(handle)
        if type(handle) is TextIOWrapper:
            if handle.name.endswith(('.gz','.bz')):
                raise Exception("Compressed files are currently not supported!")
            self.handle = handle

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