[Biopython-dev] Martel-0.35

[Andrew Dalke]

Okay, over the weekend I ended up not doing the work I was paid for
and instead worked on Martel.  It's available as usual from
http://www.biopython.org/~dalke/Martel .  This is version 0.35.
Here's the change log from the README:

  Migrated to Python 2.0 and its xml package.  No longer runs under
  older (1.x) Pythons.

  Added more RecordReaders (Until, CountLines, Nothing, Everything).

  Changed the RecordReader protocol to seed the line buffer (in the
  constructor) and to get the final state for the input file and line
  buffer (using remainder()).  Needed to allow chaining of different
  reader types as with headers and footers.

  Added a HeaderFooter Parser for formats like Prosite and PIR which
  have a header and/or a footer with records in between.

  Renamed the StateTable exception to Parser exceptions and removed the
  EOF exception.

  Experimental Iterator support ("make_iterator") as an alternate for
  the pure SAX callback method.

  Improved error reporting.  make_parser and make_iterator takes an
  optional "debug_level".  Better error location is available with
  debug_level == 1 and if it == 2, print current match information to
  stdout.  Warning: debug_level == 1 is about 11 times slower than
  debug_level == 0, which is why it is off by default.

  Support for both the 1.1 and 1.2 mxTextTools.


For people like Brad who are learning how to use Martel, try
"expression.make_parser(debug_level = 1)" or debug_level = 2.  That
really helps pin down where an error is likely located.

BTW, I started a Prosite parser.  The documentation isn't all that
helpful, and I've already found a few errors.  For example,
in the prosite 39 release, PTS_EIIA_2 has a 5 digit date!  (Interestingly,
the online version from expasy.ch has only 4 digits but the INFO
UPDATE is from 1995.)

                    Andrew
                    dalke at acm.org