Python array_tree_dict_from_reader Examples

Example #1

def main():
    input_fname = sys.argv[1]
    out_fname = sys.argv[2]

    reader = BedGraphReader( open( input_fname ) )

    # Fill array from reader
    d = array_tree_dict_from_reader( reader, {}, block_size=BLOCK_SIZE )

    for array_tree in d.itervalues():
        array_tree.root.build_summary()

    FileArrayTreeDict.dict_to_file( d, open( out_fname, "w" ) )

Example #2

File: wiggle_to_array_tree.py Project: yuzhenpeng/bx-python

def main():

    sizes_fname = sys.argv[1]
    out_fname = sys.argv[2]

    sizes = {}
    for line in open(sizes_fname):
        fields = line.split()
        sizes[fields[0]] = int(fields[1])

    # Fill array from wiggle
    d = array_tree_dict_from_reader(WiggleReader(sys.stdin), sizes)

    for value in d.values():
        value.root.build_summary()

    with open(out_fname, "w") as f:
        FileArrayTreeDict.dict_to_file(d, f)