[BioPython] my brief adventures with 1.00a4 on windows

[Michael George Lerner]

Hi,

I just downloaded biopython-1.00a4.zip from www.biopython.org.  I'm
running Windows XP with ActiveState's ActivePython 2.1.1.  I also grabbed
the base mx tools from
www.lemburg.com/files/python/3Genix-mx-Extensions.html.

As a side note, the download page at biopython.org points you at
www.lemburg.com/files/python/mxExtensions.html, where there is a note
telling you to go to the 3Genix-mx-Extensions.html page instead.  Should
the link at www.biopython.org/Download/ be updated?

Anyway, back to biopython .. I tried to work through one of the GenBank
examples in the tutorial/cookbook (which is a *wonderful* document ..
thanks!) with the following results:


ActivePython 2.1.1, build 212 (ActiveState)
Python 2.1.1 (#20, Jul 26 2001, 11:38:51) [MSC 32 bit (Intel)] on win32
Type "copyright", "credits" or "license" for more information.
>>> from Bio import GenBank
>>> gi_list = GenBank.search_for("Opuntia AND rpl16")
>>> ncbi_dict = GenBank.NCBIDictionary(parser = GenBank.RecordParser())
>>> f = ncbi_dict[gi_list[0]]
Traceback (most recent call last):
  File "<stdin>", line 1, in ?
  File "C:\Python21\Bio\GenBank\__init__.py", line 1555, in __getitem__
    return self.parser.parse(handle)
  File "C:\Python21\Bio\GenBank\__init__.py", line 289, in parse
    self._scanner.feed(handle, self._consumer)
  File "C:\Python21\Bio\GenBank\__init__.py", line 1250, in feed
    self._parser.parseFile(handle)
  File "C:\Python21\Martel\Parser.py", line 230, in parseFile
    self.parseString(fileobj.read())
  File "C:\Python21\Martel\Parser.py", line 258, in parseString
    self._err_handler.fatalError(result)
  File "C:\Python21\lib\xml\sax\handler.py", line 38, in fatalError
    raise exception
Martel.Parser.ParserPositionException: error parsing at or beyond character 55
>>>


Ick.  I fiddled around with a couple of things, and decided to just grab
the most recent cvs tree and install it.  After learning how to make my
own libpython21.a, I was able to build biopython with mingw with no
troubles.

Unfortunately, a few of the tests failed.  One of them was
test_GenBankFormat, which didn't look too promising.

In the end, I got everything working properly (I think!) by

1) Copying over the new version of Martel
2) Copying over Bio/Std.py
3) Copying over the newest version of genbank_format.py

Is something in 1.00a4 broken, or did I just have a weird setup?

Anyway, I think biopython is the neatest thing I've seen in a while, and
so does my fiancee, who knows next to nothing about programming, but can
now use biopython to deal with large numbers of GenBank records.

thanks,

-michael

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This isn't a democracy;|                        _  |Michael Lerner
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