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1 #!/usr/bin/env python
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2
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3 import os
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4 import sys
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5 from optparse import OptionParser
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6 import genome_diversity as gd
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7
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8 def main_function( parse_arguments=None ):
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9 if parse_arguments is None:
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10 parse_arguments = lambda arguments: ( None, arguments )
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11 def main_decorator( to_decorate ):
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12 def decorated_main( arguments=None ):
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13 if arguments is None:
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14 arguments = sys.argv
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15 options, arguments = parse_arguments( arguments )
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16 rc = 1
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17 try:
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18 rc = to_decorate( options, arguments )
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19 except Exception, err:
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20 sys.stderr.write( 'ERROR: %s\n' % str( err ) )
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21 traceback.print_exc()
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22 finally:
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23 sys.exit( rc )
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24 return decorated_main
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25 return main_decorator
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26
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27 def parse_arguments( arguments ):
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28 parser = OptionParser()
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29 parser.add_option('--input',
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30 type='string', dest='input',
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31 help='file of selected SNPs')
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32 parser.add_option('--output',
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33 type='string', dest='output',
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34 help='output file')
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35 parser.add_option('--snps_loc',
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36 type='string', dest='snps_loc',
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37 help='snps .loc file')
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38 parser.add_option('--scaffold_col',
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39 type="int", dest='scaffold_col',
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40 help='scaffold column in the input file')
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41 parser.add_option('--pos_col',
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42 type="int", dest='pos_col',
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43 help='position column in the input file')
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44 parser.add_option('--output_format',
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45 type="string", dest='output_format',
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46 help='output format, fasta or primer3')
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47 parser.add_option('--species',
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48 type="string", dest='species',
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49 help='species')
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50 return parser.parse_args( arguments[1:] )
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51
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52
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53 @main_function( parse_arguments )
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54 def main( options, arguments ):
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55 if not options.input:
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56 raise RuntimeError( 'missing --input option' )
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57 if not options.output:
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58 raise RuntimeError( 'missing --output option' )
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59 if not options.snps_loc:
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60 raise RuntimeError( 'missing --snps_loc option' )
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61 if not options.scaffold_col:
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62 raise RuntimeError( 'missing --scaffold_col option' )
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63 if not options.pos_col:
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64 raise RuntimeError( 'missing --pos_col option' )
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65 if not options.output_format:
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66 raise RuntimeError( 'missing --output_format option' )
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67 if not options.species:
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68 raise RuntimeError( 'missing --species option' )
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69
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70 snps = gd.SnpFile( filename=options.input, seq_col=int( options.scaffold_col ), pos_col=int( options.pos_col ) )
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71
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72 out_fh = gd._openfile( options.output, 'w' )
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73
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74 snpcalls_file = gd.get_filename_from_loc( options.species, options.snps_loc )
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75 file_root, file_ext = os.path.splitext( snpcalls_file )
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76 snpcalls_index_file = file_root + ".cdb"
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77 snpcalls = gd.SnpcallsFile( data_file=snpcalls_file, index_file=snpcalls_index_file )
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78
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79 while snps.next():
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80 seq, pos = snps.get_seq_pos()
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81 flanking_dna = snpcalls.get_flanking_dna( sequence=seq, position=pos, format=options.output_format )
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82 if flanking_dna:
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83 out_fh.write( flanking_dna )
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84
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85 out_fh.close()
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86
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87 if __name__ == "__main__":
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88 main()
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89
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