Mailinglist Archive: opensuse (1473 mails)

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Re: [opensuse] does SuSE provide a Python debugger
  • From: Josef Reidinger <jreidinger@xxxxxxx>
  • Date: Fri, 12 Jun 2009 17:33:35 +0200
  • Message-id: <4A32754F.3060404@xxxxxxx>
Maura Monville wrote:
I was given a python script that should *in theory* extract some miRNA
and target genes from the miRecords database ... I launched it but it does
not work. It prints out a lot of errors that I cannot
understand.
Does SuSE provide a debugger for python scripts ?

I never learnt Python and have to start using it ... sigh ...
The output of the attached Python script should be CSV file.
The way to run it is from command line (according to what its author stated):

# python miRecordsParser.py http://mirecords.umn.edu/miRecords

In the following I have pasted the error messages I am getting. I cannot
figure out what causes them.

Thank you very much in advance to anyone who can help me out of my misery.
Maura

# python miRecordsParser.py http://mirecords.umn.edu/miRecords/
Traceback (most recent call last):
File "miRecordsParser.py", line 284, in <module>
parser.feed(data.read())
File "/System/Library/Frameworks/
Python.framework/Versions/2.5/lib/python2.5/sgmllib.py", line 99, in feed
self.goahead(0)
File
"/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/sgmllib.py",
line 138, in goahead
k = self.parse_endtag(i)
File
"/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/sgmllib.py",
line 315, in parse_endtag
self.finish_endtag(tag)
File
"/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/sgmllib.py",
line 369, in finish_endtag
self.handle_endtag(tag, method)
File
"/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/sgmllib.py",
line 380, in handle_endtag
method()
File "miRecordsParser.py", line 126, in end_td
data = u"".join(self.temp)
UnicodeDecodeError: 'ascii' codec can't decode byte 0xa0 in position 0:
ordinal not in range(128)




I think that your problem is related to unicode character, where
expected ascii (my decode of error).
Python debugger I cannot find officially packed, but if you search
http://software.opensuse.org/search keyword pydb you find that someone
already has it in home (on your own danger).
JR
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