[BioPython] BioPython and Zope.

[Cymon Cox]

Hi Cristian,

When you add an External Method to your Zope application you assign it
directly to a function contained in a module. I don't think the imports
at the module level are never made.

In short try:

def SequenceRead(SequenceString):
	import StringIO
	from Bio import SeqRecord
	from Bio import FASTA 
	input = StringIO.StringIO(SequenceString)
	reader = FASTA.FastaReader(input)   # Error line
	seq = reader.next()
etc...

Cheers, Cymon



On Mon, 2004-04-19 at 17:28, Cristian S. Rocha wrote:
> Hello everybody,
> 
> I'm trying to parse fasta string input using Zope. I made a Zope
> external method to interface with BioPython modules. This method work
> fine on command line, but It don't work in Zope.
> 
> The code is:
> 
> ----------------
> import StringIO
> from Bio import SeqRecord
> from Bio.SeqIO import FASTA
> 
> def SequenceRead(SequenceString):
> 	input = StringIO.StringIO(SequenceString)
> 	reader = FASTA.FastaReader(input)   # Error line
> 	seq = reader.next()
> 	while seq:
> 		print "> %s" % seq.id
> 	 	seq = reader.next()
> 	return "!"
> 
> if __name__ == "__main__":
> 	print BioTools(
> """>123
> ATAGGGGATGATAGGAT
> >456
> GGATGAGGAGCGATGCG
> """
> 	)
> ----------------
> 
> The error is:
> 
> AttributeError: 'module' object has no attribute 'FastaReader'
> 
> The traceback is:
> 
> """
> Traceback (innermost last):
>   Module ZPublisher.Publish, line 98, in publish
>   Module ZPublisher.mapply, line 88, in mapply
>   Module ZPublisher.Publish, line 39, in call_object
>   Module OFS.DTMLMethod, line 127, in __call__
>   Module DocumentTemplate.DT_String, line 474, in __call__
>   Module DocumentTemplate.DT_Try, line 140, in render
>   Module DocumentTemplate.DT_Try, line 183, in render_try_except
>   Module DocumentTemplate.DT_Util, line 201, in eval
>    - __traceback_info__: SequenceText
>   Module <string>, line 1, in <expression>
>   Module Shared.DC.Scripts.Bindings, line 306, in __call__
>   Module Shared.DC.Scripts.Bindings, line 343, in _bindAndExec
>   Module Products.PythonScripts.PythonScript, line 307, in _exec
>   Module None, line 15, in Translate
>    - <PythonScript at /biodb/TranslateSequence/Translate>
>    - Line 15
>   Module Products.ExternalMethod.ExternalMethod, line 224, in __call__
>    - __traceback_info__: (('> Input.\r\nATGATGA\r\n> Output\r\nATGGGGAT',), {}, None)
>   Module /usr/lib/zope/Extensions/BioTools.py, line 9, in SequenceRead
> AttributeError: 'module' object has no attribute 'FastaReader'
> """
> 
> Do you have any idea why it's happening?
> 
> Thanks,
> Cristian.
-- 
Cymon Cox <cymon at duke.edu>
Duke University