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import os, sys
_open = open # rename for internal use -- gets redefined below
def open(dbname, mode = "r"):
text = _open(os.path.join(dbname, "config.dat"), "rb").read()
line = text.split("\n")[0]
if line == "index\tBerkeleyDB/1":
import BerkeleyDB
return BerkeleyDB.open(dbname, mode)
elif line == "index\tflat/1":
import FlatDB
return FlatDB.open(dbname, mode)
raise TypeError("Unknown index type: %r" % (line,))
def main():
from Bio import Std
import XPath
import FlatDB
XPath.xpath_index(
#dbname = "sprot_flat",
dbname = "sprot_small",
filenames = ["/home/dalke/ftps/swissprot/smaller_sprot38.dat",
#filenames = ["/home/dalke/ftps/swissprot/sprot38.dat",
],
primary_namespace = "entry",
extract_info = [
("entry", "//entry_name"),
("accession", "//%s[@type='accession']" % (Std.dbid.tag,)),
],
#creator_factory = FlatDB.CreateFlatDB,
)
if __name__ == "__main__":
main()
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