|
0
|
1 #!/usr/bin/env python
|
|
|
2
|
|
|
3 import os
|
|
|
4 import sys
|
|
|
5 from optparse import OptionParser
|
|
|
6 import genome_diversity as gd
|
|
|
7
|
|
|
8 def main_function( parse_arguments=None ):
|
|
|
9 if parse_arguments is None:
|
|
|
10 parse_arguments = lambda arguments: ( None, arguments )
|
|
|
11 def main_decorator( to_decorate ):
|
|
|
12 def decorated_main( arguments=None ):
|
|
|
13 if arguments is None:
|
|
|
14 arguments = sys.argv
|
|
|
15 options, arguments = parse_arguments( arguments )
|
|
|
16 rc = 1
|
|
|
17 try:
|
|
|
18 rc = to_decorate( options, arguments )
|
|
|
19 except Exception, err:
|
|
|
20 sys.stderr.write( 'ERROR: %s\n' % str( err ) )
|
|
|
21 traceback.print_exc()
|
|
|
22 finally:
|
|
|
23 sys.exit( rc )
|
|
|
24 return decorated_main
|
|
|
25 return main_decorator
|
|
|
26
|
|
|
27 def parse_arguments( arguments ):
|
|
|
28 parser = OptionParser()
|
|
|
29 parser.add_option('--input',
|
|
|
30 type='string', dest='input',
|
|
|
31 help='file of selected SNPs')
|
|
|
32 parser.add_option('--output',
|
|
|
33 type='string', dest='output',
|
|
|
34 help='output file')
|
|
|
35 parser.add_option('--primers_loc',
|
|
|
36 type='string', dest='primers_loc',
|
|
|
37 help='primers .loc file')
|
|
|
38 parser.add_option('--scaffold_col',
|
|
|
39 type="int", dest='scaffold_col',
|
|
|
40 help='scaffold column in the input file')
|
|
|
41 parser.add_option('--pos_col',
|
|
|
42 type="int", dest='pos_col',
|
|
|
43 help='position column in the input file')
|
|
|
44 parser.add_option('--species',
|
|
|
45 type="string", dest='species',
|
|
|
46 help='species')
|
|
|
47 return parser.parse_args( arguments[1:] )
|
|
|
48
|
|
|
49
|
|
|
50 @main_function( parse_arguments )
|
|
|
51 def main( options, arguments ):
|
|
|
52 if not options.input:
|
|
|
53 raise RuntimeError( 'missing --input option' )
|
|
|
54 if not options.output:
|
|
|
55 raise RuntimeError( 'missing --output option' )
|
|
|
56 if not options.primers_loc:
|
|
|
57 raise RuntimeError( 'missing --primers_loc option' )
|
|
|
58 if not options.scaffold_col:
|
|
|
59 raise RuntimeError( 'missing --scaffold_col option' )
|
|
|
60 if not options.pos_col:
|
|
|
61 raise RuntimeError( 'missing --pos_col option' )
|
|
|
62 if not options.species:
|
|
|
63 raise RuntimeError( 'missing --species option' )
|
|
|
64
|
|
|
65 snps = gd.SnpFile( filename=options.input, seq_col=int( options.scaffold_col ), pos_col=int( options.pos_col ) )
|
|
|
66
|
|
|
67 out_fh = gd._openfile( options.output, 'w' )
|
|
|
68
|
|
|
69 primer_data_file = gd.get_filename_from_loc( options.species, options.primers_loc )
|
|
|
70
|
|
|
71 file_root, file_ext = os.path.splitext( primer_data_file )
|
|
|
72 primer_index_file = file_root + ".cdb"
|
|
|
73 primers = gd.PrimersFile( data_file=primer_data_file, index_file=primer_index_file )
|
|
|
74
|
|
|
75 while snps.next():
|
|
|
76 seq, pos = snps.get_seq_pos()
|
|
|
77 primer = primers.get_entry( seq, pos )
|
|
|
78 if primer:
|
|
|
79 out_fh.write( primer )
|
|
|
80
|
|
|
81 out_fh.close()
|
|
|
82
|
|
|
83 if __name__ == "__main__":
|
|
|
84 main()
|
|
|
85
|
