--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/extract_flanking_dna.py	Fri Sep 28 11:35:56 2012 -0400
@@ -0,0 +1,89 @@
+#!/usr/bin/env python
+
+import os
+import sys
+from optparse import OptionParser
+import genome_diversity as gd
+
+def main_function( parse_arguments=None ):
+    if parse_arguments is None:
+        parse_arguments = lambda arguments: ( None, arguments )
+    def main_decorator( to_decorate ):
+        def decorated_main( arguments=None ):
+            if arguments is None:
+                arguments = sys.argv
+            options, arguments = parse_arguments( arguments )
+            rc = 1
+            try:
+                rc = to_decorate( options, arguments )
+            except Exception, err:
+                sys.stderr.write( 'ERROR: %s\n' % str( err ) )
+                traceback.print_exc()
+            finally:
+                sys.exit( rc )
+        return decorated_main
+    return main_decorator
+
+def parse_arguments( arguments ):
+    parser = OptionParser()
+    parser.add_option('--input',
+                        type='string', dest='input',
+                        help='file of selected SNPs')
+    parser.add_option('--output',
+                        type='string', dest='output',
+                        help='output file')
+    parser.add_option('--snps_loc',
+                        type='string', dest='snps_loc',
+                        help='snps .loc file')
+    parser.add_option('--scaffold_col',
+                        type="int", dest='scaffold_col',
+                        help='scaffold column in the input file')
+    parser.add_option('--pos_col',
+                        type="int", dest='pos_col',
+                        help='position column in the input file')
+    parser.add_option('--output_format',
+                        type="string", dest='output_format',
+                        help='output format, fasta or primer3')
+    parser.add_option('--species',
+                        type="string", dest='species',
+                        help='species')
+    return parser.parse_args( arguments[1:] )
+
+
+@main_function( parse_arguments )
+def main( options, arguments ):
+    if not options.input:
+        raise RuntimeError( 'missing --input option' )
+    if not options.output:
+        raise RuntimeError( 'missing --output option' )
+    if not options.snps_loc:
+        raise RuntimeError( 'missing --snps_loc option' )
+    if not options.scaffold_col:
+        raise RuntimeError( 'missing --scaffold_col option' )
+    if not options.pos_col:
+        raise RuntimeError( 'missing --pos_col option' )
+    if not options.output_format:
+        raise RuntimeError( 'missing --output_format option' )
+    if not options.species:
+        raise RuntimeError( 'missing --species option' )
+    
+    snps = gd.SnpFile( filename=options.input, seq_col=int( options.scaffold_col ), pos_col=int( options.pos_col ) )
+
+    out_fh = gd._openfile( options.output, 'w' )
+
+    snpcalls_file = gd.get_filename_from_loc( options.species, options.snps_loc )
+    file_root, file_ext = os.path.splitext( snpcalls_file )
+    snpcalls_index_file = file_root + ".cdb"
+    snpcalls = gd.SnpcallsFile( data_file=snpcalls_file, index_file=snpcalls_index_file )
+
+    while snps.next():
+        seq, pos = snps.get_seq_pos()
+        flanking_dna = snpcalls.get_flanking_dna( sequence=seq, position=pos, format=options.output_format )
+        if flanking_dna:
+            out_fh.write( flanking_dna )
+
+    out_fh.close()
+
+if __name__ == "__main__":
+    main()
+