diff tools/maf/maf_limit_size.py @ 0:9071e359b9a3

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/maf/maf_limit_size.py	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,36 @@
+#!/usr/bin/env python
+#Dan Blankenberg
+"""
+Removes blocks that fall outside of specified size range.
+"""
+
+import sys
+from galaxy import eggs
+import pkg_resources; pkg_resources.require( "bx-python" )
+import bx.align.maf
+
+assert sys.version_info[:2] >= ( 2, 4 )
+
+def __main__():
+
+    input_maf_filename = sys.argv[1].strip()
+    output_filename1 = sys.argv[2].strip()
+    min_size = int( sys.argv[3].strip() )
+    max_size = int( sys.argv[4].strip() )
+    if max_size < 1: max_size = sys.maxint
+    maf_writer = bx.align.maf.Writer( open( output_filename1, 'w' ) )
+    try:
+        maf_reader = bx.align.maf.Reader( open( input_maf_filename, 'r' ) )
+    except:
+        print >>sys.stderr, "Your MAF file appears to be malformed."
+        sys.exit()
+    
+    blocks_kept = 0
+    i = 0
+    for i, m in enumerate( maf_reader ):
+        if min_size <= m.text_size <= max_size:
+            maf_writer.write( m )
+            blocks_kept += 1
+    print 'Kept %s of %s blocks (%.2f%%).' % ( blocks_kept, i + 1, float( blocks_kept ) / float( i + 1 ) * 100.0 )
+
+if __name__ == "__main__": __main__()