--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/get_flanks.py	Tue Apr 01 10:51:10 2014 -0400
@@ -0,0 +1,189 @@
+#!/usr/bin/env python
+#Done by: Guru
+
+"""
+Get Flanking regions.
+
+usage: %prog input out_file size direction region
+   -l, --cols=N,N,N,N: Columns for chrom, start, end, strand in file
+   -o, --off=N: Offset
+"""
+
+import sys, re, os
+from bx.cookbook import doc_optparse
+from galaxy.tools.util.galaxyops import *
+
+def stop_err( msg ):
+    sys.stderr.write( msg )
+    sys.exit()
+
+def main(): 
+    try:
+        if int( sys.argv[3] ) < 0:
+            raise Exception
+    except:
+        stop_err( "Length of flanking region(s) must be a non-negative integer." )
+
+    # Parsing Command Line here
+    options, args = doc_optparse.parse( __doc__ )
+    try:
+        chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols )
+        inp_file, out_file, size, direction, region = args
+        if strand_col_1 <= 0:
+            strand = "+"        #if strand is not defined, default it to +
+    except:
+        stop_err( "Metadata issue, correct the metadata attributes by clicking on the pencil icon in the history item." )
+    try:
+        offset = int(options.off)
+        size = int(size)
+    except:    
+        stop_err( "Invalid offset or length entered. Try again by entering valid integer values." )
+
+    fo = open(out_file,'w')
+    
+    skipped_lines = 0
+    first_invalid_line = 0
+    invalid_line = None
+    elems = []
+    j=0
+    for i, line in enumerate( file( inp_file ) ):
+        line = line.strip()
+        if line and (not line.startswith( '#' )) and line != '':
+            j+=1
+            try:
+                elems = line.split('\t')
+                #if the start and/or end columns are not numbers, skip that line.
+                assert int(elems[start_col_1])
+                assert int(elems[end_col_1])
+                if strand_col_1 != -1:
+                    strand = elems[strand_col_1]
+                #if the stand value is not + or -, skip that line.
+                assert strand in ['+', '-']
+                if direction == 'Upstream':
+                    if strand == '+':
+                        if region == 'end':
+                            elems[end_col_1] = str(int(elems[end_col_1]) + offset)
+                            elems[start_col_1] = str( int(elems[end_col_1]) - size )
+                        else:
+                            elems[end_col_1] = str(int(elems[start_col_1]) + offset)
+                            elems[start_col_1] = str( int(elems[end_col_1]) - size )
+                    elif strand == '-':
+                        if region == 'end':
+                            elems[start_col_1] = str(int(elems[start_col_1]) - offset)
+                            elems[end_col_1] = str(int(elems[start_col_1]) + size)
+                        else:
+                            elems[start_col_1] = str(int(elems[end_col_1]) - offset)
+                            elems[end_col_1] = str(int(elems[start_col_1]) + size)
+                    assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0
+                    fo.write( "%s\n" % '\t'.join( elems ) )
+                                
+                elif direction == 'Downstream':
+                    if strand == '-':
+                        if region == 'start':
+                           elems[end_col_1] = str(int(elems[end_col_1]) - offset)
+                           elems[start_col_1] = str( int(elems[end_col_1]) - size )
+                        else:
+                           elems[end_col_1] = str(int(elems[start_col_1]) - offset)
+                           elems[start_col_1] = str( int(elems[end_col_1]) - size )
+                    elif strand == '+':
+                        if region == 'start':
+                            elems[start_col_1] = str(int(elems[start_col_1]) + offset)
+                            elems[end_col_1] = str(int(elems[start_col_1]) + size)
+                        else:
+                            elems[start_col_1] = str(int(elems[end_col_1]) + offset)
+                            elems[end_col_1] = str(int(elems[start_col_1]) + size)
+                    assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0
+                    fo.write( "%s\n" % '\t'.join( elems ) )
+                    
+                elif direction == 'Both':
+                    if strand == '-':
+                        if region == 'start':
+                            start = str(int(elems[end_col_1]) - offset)
+                            end1 = str(int(start) + size)
+                            end2 = str(int(start) - size)
+                            elems[start_col_1]=start
+                            elems[end_col_1]=end1
+                            assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0
+                            fo.write( "%s\n" % '\t'.join( elems ) )
+                            elems[start_col_1]=end2
+                            elems[end_col_1]=start
+                            assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0
+                            fo.write( "%s\n" % '\t'.join( elems ) )
+                        elif region == 'end':
+                            start = str(int(elems[start_col_1]) - offset)
+                            end1 = str(int(start) + size)
+                            end2 = str(int(start) - size)
+                            elems[start_col_1]=start
+                            elems[end_col_1]=end1
+                            assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0
+                            fo.write( "%s\n" % '\t'.join( elems ) )
+                            elems[start_col_1]=end2
+                            elems[end_col_1]=start
+                            assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0
+                            fo.write( "%s\n" % '\t'.join( elems ) )
+                        else:
+                            start1 = str(int(elems[end_col_1]) - offset)
+                            end1 = str(int(start1) + size)
+                            start2 = str(int(elems[start_col_1]) - offset)
+                            end2 = str(int(start2) - size)
+                            elems[start_col_1]=start1
+                            elems[end_col_1]=end1
+                            assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0
+                            fo.write( "%s\n" % '\t'.join( elems ) )
+                            elems[start_col_1]=end2
+                            elems[end_col_1]=start2
+                            assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0
+                            fo.write( "%s\n" % '\t'.join( elems ) )
+                    elif strand == '+':
+                        if region == 'start':
+                            start = str(int(elems[start_col_1]) + offset)
+                            end1 = str(int(start) - size)
+                            end2 = str(int(start) + size)
+                            elems[start_col_1]=end1
+                            elems[end_col_1]=start
+                            assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0
+                            fo.write( "%s\n" % '\t'.join( elems ) )
+                            elems[start_col_1]=start
+                            elems[end_col_1]=end2
+                            assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0
+                            fo.write( "%s\n" % '\t'.join( elems ) )
+                        elif region == 'end':
+                            start = str(int(elems[end_col_1]) + offset)
+                            end1 = str(int(start) - size)
+                            end2 = str(int(start) + size)
+                            elems[start_col_1]=end1
+                            elems[end_col_1]=start
+                            assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0
+                            fo.write( "%s\n" % '\t'.join( elems ) )
+                            elems[start_col_1]=start
+                            elems[end_col_1]=end2
+                            assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0
+                            fo.write( "%s\n" % '\t'.join( elems ) )
+                        else:
+                            start1 = str(int(elems[start_col_1]) + offset)
+                            end1 = str(int(start1) - size)
+                            start2 = str(int(elems[end_col_1]) + offset)
+                            end2 = str(int(start2) + size)
+                            elems[start_col_1]=end1
+                            elems[end_col_1]=start1
+                            assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0
+                            fo.write( "%s\n" % '\t'.join( elems ) )
+                            elems[start_col_1]=start2
+                            elems[end_col_1]=end2
+                            assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0
+                            fo.write( "%s\n" % '\t'.join( elems ) )
+            except:
+                skipped_lines += 1
+                if not invalid_line:
+                    first_invalid_line = i + 1
+                    invalid_line = line
+    fo.close()
+
+    if skipped_lines == j:
+        stop_err( "Data issue: click the pencil icon in the history item to correct the metadata attributes." )
+    if skipped_lines > 0:
+        print 'Skipped %d invalid lines starting with #%dL "%s"' % ( skipped_lines, first_invalid_line, invalid_line )
+    print 'Location: %s, Region: %s, Flank-length: %d, Offset: %d ' %( direction, region, size, offset )
+    
+if __name__ == "__main__":
+    main()