root/galaxy-central/lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py @ 2

#!/usr/bin/env python

from __future__ import division

import sys
from galaxy import eggs
import pkg_resources; pkg_resources.require( "bx-python" )
from bx.arrays.array_tree import *
# from bx.arrays.wiggle import BedReader

BLOCK_SIZE = 100

class BedGraphReader:
    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
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" ) )

if __name__ == "__main__": 
    main()