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bx-python / scripts / wiggle_to_simple.py

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#!/usr/bin/env python

"""
Read a wiggle track and print out a series of lines containing
"chrom position score". Ignores track lines, handles bed, variableStep
and fixedStep wiggle lines.
"""

import psyco_full

import sys
import bx.wiggle

if len( sys.argv ) > 1: in_file = open( sys.argv[1] )
else: in_file = sys.stdin

if len( sys.argv ) > 2: out_file = open( sys.argv[2], "w" )
else: out_file = sys.stdout

for fields in bx.wiggle.Reader( in_file ):
    print " ".join( map( str, fields ) )

in_file.close()
out_file.close()