[Biopython-dev] [Bug 2480] Local BLAST fails: Spaces in Windows file-path values

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2480





------- Comment #37 from drpatnaik at yahoo.com  2008-10-11 01:08 EST -------
Thank you. Confirming that CVS version 1.82 of the file works fine on Windows
XP SP2 with Python 2.5.2.

A note:

  A custom script using Bio/Blast can appear to hang, and the results file
truncated, if the 'error handle' is used before the 'result handle':

  res_hdl, err_hdl = NCBIStandalone.blastall(my_blast, 'blastn', my_db, my_seq)

  # OK
  my_result = res_hdl.read()
  my_error = err_hdl.read()

  # Not OK
  my_error = err_hdl.read()
  my_result = res_hdl.read()

Some recapitulated notes:

  1. File-names, file-paths, or database values can contain spaces.

  2. There is no special, Windows-specific requirement to use backslash (\) as
the directory separator.

  3. There is no special, Windows-specific requirement to enclose a value
inside double-quotes (") instead of single-quotes ('), or to use Python's 'r'.

  4. Except for database values, DOS 8.3 file-names (short file-names) can be
used.

  5. If the database value contains a space, it should be enclosed in
double-quotes (").

  6. If the database value refers to multiple databases, and at least one of
them has a space in it, then the pointer for that database should be
additionally enclosed in backslash-escaped double-quotes (\").


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