[Biopython-dev] need help with Genbank

[Dinakar Desai]

Jeffrey Chang wrote:
> The GenBank parser has gone through a few revisions to handle format
> changes since 1.00a4 was released.  Try getting the latest version out
> of CVS (cvs.open-bio.org) and see if that fixes the problem.
> 
> Otherwise, please send in a sample GenBank record that causes the
> parser to break.
> 
> Jeff
> 
> 
> 
> 
> On Thu, Jul 18, 2002 at 11:02:41AM -0500, Dinakar Desai wrote:
> 
>>Hello:
>>
>>I have install biopython1.004a and python 2.2.1 on linux box. I am going 
>>through tutorial written by Brad et al. (very good work).
>>With following code I get trace back which I have pasted at the end.
>>Can someone help me with.  I must be dong something wrong here.
>>
>>Thanks
>>
>>Dinakar
>><code>
>>	30 from Bio import GenBank
>>      31 record_file = open('record_file.seq', 'w+')
>>      32 record_parser = GenBank.FeatureParser()
>>      33 ncbi_dict = GenBank.NCBIDictionary()
>>      34 for id in titles:
>>      35   gb_seqrecord = ncbi_dict[id]
>>      36   record_file.write( gb_seqrecord)
>>      37
>>      38
>>      39 record_file.close()
>>      40 record_file = open('record_file.seq', 'r')
>>      41 gb_iter = GenBank.Iterator(record_file, record_parser)
>>      42 while 1:
>>      43   current_record = gb_iter.next()
>>      44   if current_record is None:
>>      45     break
>>      46   print current_record.seq
>>      47   print current_record.source
>>      48   print current_record.author
>>      49 record_file.close()
>>
>></code>
>><traceback>
>>Traceback (most recent call last):
>>   File "./test_as.py", line 43, in ?
>>     current_record = gb_iter.next()
>>   File 
>>"/home/desas2/lib/python2.2/site-packages/Bio/GenBank/__init__.py", linet
>>     return self._parser.parse(File.StringHandle(data))
>>   File 
>>"/home/desas2/lib/python2.2/site-packages/Bio/GenBank/__init__.py", linee
>>     self._scanner.feed(handle, self._consumer)
>>   File 
>>"/home/desas2/lib/python2.2/site-packages/Bio/GenBank/__init__.py", lined
>>     self._parser.parseFile(handle)
>>   File "/home/desas2/lib/python2.2/site-packages/Martel/Parser.py", 
>>line 230, ie
>>     self.parseString(fileobj.read())
>>   File "/home/desas2/lib/python2.2/site-packages/Martel/Parser.py", 
>>line 258, ig
>>     self._err_handler.fatalError(result)
>>   File "/home/desas2/lib/python2.2/xml/sax/handler.py", line 38, in 
>>fatalError
>>     raise exception
>>Martel.Parser.ParserPositionException: error parsing at or beyond 
>>character 55
>>
>></traceback>
>>-- 
>>
>>
>>_______________________________________________
>>Biopython-dev mailing list
>>Biopython-dev at biopython.org
>>http://biopython.org/mailman/listinfo/biopython-dev
> 

Hello Jeff:

Thanks for your email. I downloaded cvs version of biopython. I install 
numarray0.3.5. I get the following error message when I tried to install 
  biopython with following command:
python setup.py install

<error_msg>
  building 'Bio.Tools.KDTree._KDTreecmodule' extension
   skipping Bio/Tools/KDTree/_KDTree.C (build/temp.linux-i686-2.2/_KDTree.o
  g -O3 -Wall -Wstrict-prototypes -fPIC -I/home/desas2/inclu
de/python2.2 -c Bio/Tools/KDTree/_KDTree.swig.C -o 
build/temp.linux-i686-2.2/_KD
Tree.swig.o
</error_msg>

Please let me know what else I need to install to fix this problem of 
install of cvs version of biopython.

Thank you very much for your time.

Dinakar


-- 

Dinakar Desai, Ph.D
Phone: 289-3972/266-2831

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----------------------

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