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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

BLOCK_SIZE = 100


[docs]class BedGraphReader:
[docs] def __init__( self, f ): self.f = f
def __iter__( self ): return self
[docs] 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.itervalues(): array_tree.root.build_summary() FileArrayTreeDict.dict_to_file( d, open( out_fname, "w" ) )
if __name__ == "__main__": main()