[BioPython] my brief adventures with 1.00a4 on windows
Michael George Lerner
mlerner@umich.edu
Mon, 11 Feb 2002 15:35:05 -0500 (EST)
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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