#!/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.
"""
import sys
from galaxy import eggs
import pkg_resources; pkg_resources.require( "bx-python" )
import bx.wiggle
from galaxy.tools.exception_handling import *
[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, e:
in_file.close()
out_file.close()
stop_err( str( e ) )
in_file.close()
out_file.close()
if __name__ == "__main__": main()