sam-to-bedseq.py 文件源码

def build_sam_tags(flds):
    """
    Given a list of fields from a SAM file
    (all fields, including the first 11 fixed fields),
    returns a dictionary with the SAM tags (e.g. 'MD', 'NM').

    Tags with type 'i' are converted to integers.
    Tags with type 'f' are converted to floats.

    Example:
      tags = build_sam_tags( ["NM:i:0","MD:Z:77"])
        => tags = { 'NM':0, 'MD':'77' }
    """

    # Split tags into tuples of (name,type,value)
    # e.g. ["NM:i:0","MD:Z:77"] => [('NM', 'i', '0'), ('MD', 'Z', '77')]
    in_tags = [ tuple(x.split(':')) for x in flds[11:]]
    out_tags = {}
    for n,t,v in in_tags:
        if t=="i":
            v = int(v)
        elif t=='f':
            v = float(v)
        out_tags[n]=v
    return out_tags