Mercurial > repos > miller-lab > genome_diversity

comparison specify_restriction_enzymes.py @ 0:2c498d40ecde

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author miller-lab
date Mon, 09 Apr 2012 12:03:06 -0400
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-1:000000000000 0:2c498d40ecde
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('--enzyme_list',
45 type="string", dest='enzyme_list_string',
46 help='comma separated list of enzymes')
47 parser.add_option('--species',
48 type="string", dest='species',
49 help='species')
50 return parser.parse_args( arguments[1:] )
51
52
53 @main_function( parse_arguments )
54 def main( options, arguments ):
55 if not options.input:
56 raise RuntimeError( 'missing --input option' )
57 if not options.output:
58 raise RuntimeError( 'missing --output option' )
59 if not options.primers_loc:
60 raise RuntimeError( 'missing --primers_loc option' )
61 if not options.scaffold_col:
62 raise RuntimeError( 'missing --scaffold_col option' )
63 if not options.pos_col:
64 raise RuntimeError( 'missing --pos_col option' )
65 if not options.enzyme_list_string:
66 raise RuntimeError( 'missing --enzyme_list option' )
67 if not options.species:
68 raise RuntimeError( 'missing --species option' )
69
70 snps = gd.SnpFile( filename=options.input, seq_col=int( options.scaffold_col ), pos_col=int( options.pos_col ) )
71
72 out_fh = gd._openfile( options.output, 'w' )
73
74 enzyme_dict = {}
75 for enzyme in options.enzyme_list_string.split( ',' ):
76 enzyme = enzyme.strip()
77 if enzyme:
78 enzyme_dict[enzyme] = 1
79
80 primer_data_file = gd.get_filename_from_loc( options.species, options.primers_loc )
81 file_root, file_ext = os.path.splitext( primer_data_file )
82 primer_index_file = file_root + ".cdb"
83 primers = gd.PrimersFile( data_file=primer_data_file, index_file=primer_index_file )
84
85 comments_printed = False
86
87 while snps.next():
88 seq, pos = snps.get_seq_pos()
89 enzyme_list = primers.get_enzymes( seq, pos )
90 for enzyme in enzyme_list:
91 if enzyme in enzyme_dict:
92 if not comments_printed:
93 for comment in snps.comments:
94 out_fh.write( "%s\n" % comment )
95 comments_printed = True
96 out_fh.write( "%s\n" % snps.line )
97 break
98
99 out_fh.close()
100
101 if __name__ == "__main__":
102 main()
103