diff tools/filters/wiggle_to_simple.py @ 0:9071e359b9a3

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/filters/wiggle_to_simple.py	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,43 @@
+#!/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()