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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.ucsc import UCSCOutWrapper, UCSCLimitException


[docs]def stop_err( msg ): sys.stderr.write( msg ) sys.exit()
[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: in_file.close() out_file.close() stop_err( str( e ) ) in_file.close() out_file.close()
if __name__ == "__main__": main()