Mercurial > repos > xuebing > sharplabtool
comparison tools/stats/wiggle_to_simple.py @ 0:9071e359b9a3
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| author | xuebing |
|---|---|
| date | Fri, 09 Mar 2012 19:37:19 -0500 |
| parents | |
| children |
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| -1:000000000000 | 0:9071e359b9a3 |
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| 1 #!/usr/bin/env python | |
| 2 | |
| 3 """ | |
| 4 Read a wiggle track and print out a series of lines containing | |
| 5 "chrom position score". Ignores track lines, handles bed, variableStep | |
| 6 and fixedStep wiggle lines. | |
| 7 """ | |
| 8 import sys | |
| 9 from galaxy import eggs | |
| 10 import pkg_resources; pkg_resources.require( "bx-python" ) | |
| 11 import bx.wiggle | |
| 12 from galaxy.tools.exception_handling import * | |
| 13 | |
| 14 def stop_err( msg ): | |
| 15 sys.stderr.write( msg ) | |
| 16 sys.exit() | |
| 17 | |
| 18 def main(): | |
| 19 if len( sys.argv ) > 1: | |
| 20 in_file = open( sys.argv[1] ) | |
| 21 else: | |
| 22 in_file = open( sys.stdin ) | |
| 23 | |
| 24 if len( sys.argv ) > 2: | |
| 25 out_file = open( sys.argv[2], "w" ) | |
| 26 else: | |
| 27 out_file = sys.stdout | |
| 28 | |
| 29 try: | |
| 30 for fields in bx.wiggle.IntervalReader( UCSCOutWrapper( in_file ) ): | |
| 31 out_file.write( "%s\n" % "\t".join( map( str, fields ) ) ) | |
| 32 except UCSCLimitException: | |
| 33 # Wiggle data was truncated, at the very least need to warn the user. | |
| 34 print 'Encountered message from UCSC: "Reached output limit of 100000 data values", so be aware your data was truncated.' | |
| 35 except ValueError, e: | |
| 36 in_file.close() | |
| 37 out_file.close() | |
| 38 stop_err( str( e ) ) | |
| 39 | |
| 40 in_file.close() | |
| 41 out_file.close() | |
| 42 | |
| 43 if __name__ == "__main__": main() |