/tools/filters/wiggle_to_simple.py
https://bitbucket.org/cistrome/cistrome-harvard/ · Python · 43 lines · 32 code · 7 blank · 4 comment · 9 complexity · 8596894e29037ebcf2b704ddc78bfbad MD5 · raw file
- #!/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 sys
- from galaxy import eggs
- import pkg_resources; pkg_resources.require( "bx-python" )
- import bx.wiggle
- from galaxy.tools.exception_handling import *
- def stop_err( msg ):
- sys.stderr.write( msg )
- sys.exit()
- 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()