/tools/genome_diversity/select_restriction_enzymes.py
https://bitbucket.org/cistrome/cistrome-harvard/ · Python · 103 lines · 88 code · 14 blank · 1 comment · 20 complexity · 8e4f01529f050bca33f23c9f2d776df7 MD5 · raw file
- #!/usr/bin/env python2.5
- 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('--primers_loc',
- type='string', dest='primers_loc',
- help='primers .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('--enzyme_list',
- type="string", dest='enzyme_list_string',
- help='comma separated list of enzymes')
- 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.primers_loc:
- raise RuntimeError( 'missing --primers_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.enzyme_list_string:
- raise RuntimeError( 'missing --enzyme_list 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' )
- enzyme_dict = {}
- for enzyme in options.enzyme_list_string.split( ',' ):
- enzyme = enzyme.strip()
- if enzyme:
- enzyme_dict[enzyme] = 1
- primer_data_file = gd.get_filename_from_loc( options.species, options.primers_loc )
- file_root, file_ext = os.path.splitext( primer_data_file )
- primer_index_file = file_root + ".cdb"
- primers = gd.PrimersFile( data_file=primer_data_file, index_file=primer_index_file )
- comments_printed = False
- while snps.next():
- seq, pos = snps.get_seq_pos()
- enzyme_list = primers.get_enzymes( seq, pos )
- for enzyme in enzyme_list:
- if enzyme in enzyme_dict:
- if not comments_printed:
- for comment in snps.comments:
- out_fh.write( "%s\n" % comment )
- comments_printed = True
- out_fh.write( "%s\n" % snps.line )
- break
- out_fh.close()
- if __name__ == "__main__":
- main()