Package Bio :: Package Mindy
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Source Code for Package Bio.Mindy

 1  import os, sys 
 2   
 3  _open = open  # rename for internal use -- gets redefined below 
 4   
5 -def open(dbname, mode = "r"):
6 text = _open(os.path.join(dbname, "config.dat"), "rb").read() 7 line = text.split("\n")[0] 8 if line == "index\tBerkeleyDB/1": 9 import BerkeleyDB 10 return BerkeleyDB.open(dbname, mode) 11 elif line == "index\tflat/1": 12 import FlatDB 13 return FlatDB.open(dbname, mode) 14 15 raise TypeError("Unknown index type: %r" % (line,))
16 17
18 -def main():
19 from Bio import Std 20 import XPath 21 import FlatDB 22 XPath.xpath_index( 23 #dbname = "sprot_flat", 24 dbname = "sprot_small", 25 filenames = ["/home/dalke/ftps/swissprot/smaller_sprot38.dat", 26 #filenames = ["/home/dalke/ftps/swissprot/sprot38.dat", 27 ], 28 primary_namespace = "entry", 29 extract_info = [ 30 ("entry", "//entry_name"), 31 ("accession", "//%s[@type='accession']" % (Std.dbid.tag,)), 32 ], 33 #creator_factory = FlatDB.CreateFlatDB, 34 )
35 36 37 if __name__ == "__main__": 38 main() 39