[Biopython-dev] [Bug 1680] Problems with the GenBank indexing

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

http://bugzilla.open-bio.org/show_bug.cgi?id=1680





------- Comment #3 from biopython-bugzilla at maubp.freeserve.co.uk  2005-11-09 07:16 -------
(In reply to comment #1)
> This is because the Martel/Mindy iterator does not recognize spaces
> between the records in the file.  If you remove the spaces from the
> file, the code will index the file without complaint.
..
> One fix might be to modify the system to ignore whitespaces between
> records. But that may cause problems if the system were applied to a
> format where the number of blank lines were important.

Where is the "format" used by the Martel/Mindy iterator defined?

In the normal case, GenBank.index_file() simply calls
SimpleSeqRecord.create_flatdb() to do the work.

Does this use the same "format" for all types of file when asked to create a
flat database?




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