--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/fastq/fastq_manipulation.py	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,37 @@
+#Dan Blankenberg
+import sys, os, shutil
+import imp
+from galaxy_utils.sequence.fastq import fastqReader, fastqWriter
+
+def main():
+    #Read command line arguments
+    input_filename = sys.argv[1]
+    script_filename = sys.argv[2]
+    output_filename = sys.argv[3]
+    additional_files_path = sys.argv[4]
+    input_type = sys.argv[5] or 'sanger'
+    
+    #Save script file for debuging/verification info later
+    os.mkdir( additional_files_path )
+    shutil.copy( script_filename, os.path.join( additional_files_path, 'debug.txt' ) )
+    
+    fastq_manipulator = imp.load_module( 'fastq_manipulator', open( script_filename ), script_filename, ( '', 'r', imp.PY_SOURCE ) )
+    
+    out = fastqWriter( open( output_filename, 'wb' ), format = input_type )
+    
+    i = None
+    reads_manipulated = 0
+    for i, fastq_read in enumerate( fastqReader( open( input_filename ), format = input_type ) ):
+        new_read = fastq_manipulator.match_and_manipulate_read( fastq_read )
+        if new_read:
+            out.write( new_read )
+        if new_read != fastq_read:
+            reads_manipulated += 1
+    out.close()
+    if i is None:
+        print "Your file contains no valid FASTQ reads."
+    else:
+        print 'Manipulated %s of %s reads (%.2f%%).' % ( reads_manipulated, i + 1, float( reads_manipulated ) / float( i + 1 ) * 100.0 )
+
+if __name__ == "__main__":
+    main()