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

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





------- Comment #29 from drpatnaik at yahoo.com  2008-10-01 16:06 EST -------
It seems the BLAST executables can accept multiple databases (database
pointers) in the 'd' argument, but they need to be space-separated. When there
is a space in a single database's path-value, BLAST can interpret the provided
argument as two databases and then fail. This can be the reason why the
path-values for input sequence files and databases need to be quoted/escaped in
different ways:

  blast_db = r'"\"C:\Documents and Settings\patnaik\My
Documents\blast\bin\hairpin.db\""'

  input_seq = r'"C:\Documents and Settings\patnaik\My
Documents\blast\bin\30a.seq"

If this is correct, it might be helpful if Biopython had a functionality to
accept multiple databases (for BLAST) by using the list data-type:

  blast_db = [r'"C:\Documents and Settings\patnaik\My
Documents\blast\data\mouse.db", r'"C:\Documents and Settings\patnaik\My
Documents\blast\data\rat.db"]

Biopython can then collapse the list items into a properly quoted/escaped
string for BLAST's 'd' argument.

If this is not feasible, then a note in the documentation will also be of help.


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