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Source code for galaxy.datatypes.converters.wiggle_to_simple_converter

#!/usr/bin/env python
# code is same as ~/tools/stats/wiggle_to_simple.py
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.
from __future__ import print_function

import sys

import bx.wiggle

from galaxy.util import unicodify
from galaxy.util.ucsc import (

[docs]def stop_err(msg): sys.stderr.write(msg) sys.exit(1)
[docs]def main(): if len(sys.argv) > 1: in_file = open(sys.argv[1]) else: in_file = open(sys.stdin) if len(sys.argv) > 2: out_file = open(sys.argv[2], "w") else: out_file = sys.stdout try: for fields in bx.wiggle.IntervalReader(UCSCOutWrapper(in_file)): out_file.write("%s\n" % "\t".join(map(str, fields))) except UCSCLimitException: # Wiggle data was truncated, at the very least need to warn the user. print('Encountered message from UCSC: "Reached output limit of 100000 data values", so be aware your data was truncated.') except ValueError as e: stop_err(unicodify(e)) finally: in_file.close() out_file.close()
if __name__ == "__main__": main()