[Biopython-dev] need help with Genbank - additional error

[Dinakar Desai]

Dinakar Desai wrote:
> 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
> 
> 

To follow up:
I also had this error message at end.
<error_msg>
skipping Bio/Tools/KDTree/_KDTree.C (build/temp.linux-i686-2.2/_KDTree.o 
up-to-)
gcc -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -fPIC 
-I/home/desas2/include/pytho
Bio/Tools/KDTree/_KDTree.swig.C:748:42: Numeric/arrayobject.h: No such 
file or y
error: command 'gcc' failed with exit status 1
</error_msg>

Thanks

Dinakar

-- 

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

perl -e '$_ = "mqonx.zako\@ude";$_=~ tr /qnxzk\@.ue/npqmy.\@eu/; print'
----------------------

Everything should be made as simple as possible, but no 
simpler.-----Albert Einstein