Source code for galaxy.datatypes.converters.bedgraph_to_array_tree_converter

#!/usr/bin/env python

from __future__ import division

import sys

from bx.arrays.array_tree import array_tree_dict_from_reader, FileArrayTreeDict
from six import Iterator

BLOCK_SIZE = 100


[docs]class BedGraphReader(Iterator):
[docs]    def __init__(self, f):
        self.f = f

    def __iter__(self):
        return self

    def __next__(self):
        while True:
            line = self.f.readline()
            if not line:
                raise StopIteration()
            if line.isspace():
                continue
            if line[0] == "#":
                continue
            if line[0].isalpha():
                if line.startswith("track") or line.startswith("browser"):
                    continue

                feature = line.strip().split()
                chrom = feature[0]
                chrom_start = int(feature[1])
                chrom_end = int(feature[2])
                score = float(feature[3])
                return chrom, chrom_start, chrom_end, None, score


[docs]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.values():
        array_tree.root.build_summary()

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


if __name__ == "__main__":
    main()