Re: [BioPython] BLAST subprocess problem with a GUI

Hi Peter and the rest of the mailing list!

I'm using Biopython 1.49b and Python 2.5.

I tried your suggestion and changed \Blast\NCBIStandalone.py as you said:

        import subprocess, sys
        #We don't need to supply any piped input, but we setup the
        #pipe anyway as a work around for a python bug if this is
        #called from a Windows GUI program.  For details, see:
        #http://bugs.python.org/issue1124861
        blast_process = subprocess.Popen(cmd_string,
                                         stdin=subprocess.PIPE,
                                         stdout=subprocess.PIPE,
                                         stderr=subprocess.PIPE,
                                         shell=(sys.platform!="win32"))
        blast_process.stdin.close()
        return blast_process.stdout, blast_process.stderr

And after comipilation with py2exe it's seem to work! In addition I changed
\Application\__init__.py in function generic_run
\ClustalW\__init__.py in function do_alignment

in the same way because I got the same error message when I used Primer3 and 
ClustalW.
I tried up to now only on view Windows XP PC's but it's looks like the 
problem is solved!

Finally I can release the tool for testing! Thanks to all for their help!

Re: [BioPython] BLAST subprocess problem with a GUI

On Mon, Feb 2, 2009 at 7:37 AM, Stefanie Lück <lueck <at> ipk-gatersleben.de> wrote:
>
> Hi Peter and the rest of the mailing list!
>
> I'm using Biopython 1.49b and Python 2.5.
>
> I tried your suggestion and changed \Blast\NCBIStandalone.py as you said:
>
>       import subprocess, sys
>       #We don't need to supply any piped input, but we setup the
>       #pipe anyway as a work around for a python bug if this is
>       #called from a Windows GUI program.  For details, see:
>       #http://bugs.python.org/issue1124861
>       blast_process = subprocess.Popen(cmd_string,
>                                        stdin=subprocess.PIPE,
>                                        stdout=subprocess.PIPE,
>                                        stderr=subprocess.PIPE,
>                                        shell=(sys.platform!="win32"))
>       blast_process.stdin.close()
>       return blast_process.stdout, blast_process.stderr
>
> And after comipilation with py2exe it's seem to work! In addition I changed
> \Application\__init__.py in function generic_run
> \ClustalW\__init__.py in function do_alignment
> in the same way because I got the same error message when I used Primer3
> and ClustalW. I tried up to now only on view Windows XP PC's but it's looks
> like the problem is solved!

Great - I've made this change in CVS now:
Blast/NCBIStandalone.py revision: 1.85

[BioPython] KEGG enzyme error

Hi,

I am trying to parse KEGG enzyme. The parser is failing for    EC 1.1.1.49

The data line where it is failing is-

"DRE: 100148915 570579(wu:fj78b06)"

There are several other data lines in this format.

The error I am getting is:

line 227, in parse

    key, values = data.split(":")

ValueError: too many values to unpack

Here is my code:

import urllib

from Bio.KEGG import Enzyme

dataFile = open(myFile)

for record in Enzyme.parse(dataFile):

    print record.entry

[BioPython] 10th year

I guess everybody is too busy to notice that biopython is into its 10th
year now.. birthday celebrations are nine months away, Since the mailing
lists start in September 1999. But I guess that some sort of party at
BOSC would be nice...

--

-- 
Iddo Friedberg, Ph.D.
CALIT2 Atkinson Hall MC #0446
University of California San Diego
9500 Gilman Drive
La Jolla, CA 92093-0446 USA
+1 (858) 534-0570
http://iddo-friedberg.org

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Re: [BioPython] KEGG enzyme error

On Mon, Feb 2, 2009 at 9:33 PM, Ragini Pandey <rapandey <at> iupui.edu> wrote:
> Hi,
>
> I am trying to parse KEGG enzyme. The parser is failing for    EC 1.1.1.49
> The data line where it is failing is-
> "DRE: 100148915 570579(wu:fj78b06)"
> There are several other data lines in this format.
>
> The error I am getting is:
> line 227, in parse
>    key, values = data.split(":")
> ValueError: too many values to unpack

The problem is the code expects a single ":" character which can be
used to split the string into the key ("DRE") and the data, here
"100148915 570579(wu:fj78b06)" but the extra ":" is causing the split
to give three parts.  Try editing that line to read:
    key, values = data.split(":",1)

> Here is my code:
>
> import urllib
> from Bio.KEGG import Enzyme
> dataFile = open(myFile)
> for record in Enzyme.parse(dataFile):
>    print record.entry
>
> Would appreciate your help on this.

Which file exactly are you using?  The problem data line you gave

Re: [BioPython] KEGG enzyme error

On Tue, Feb 3, 2009 at 6:00 PM, Ragini Pandey <rapandey <at> iupui.edu> wrote:
>
> Hi Peter,
>
> The file I am trying to parse is
> ftp://ftp.genome.jp/pub/kegg/ligand/enzyme/enzyme
>
> Thanks
> Ragini

Hi Ragini,

I was able to quickly test my suggested fix on that file, and it seems
to resolve the problem.

I've checked this into CVS, see Bio/KEGG/Enzyme/__init__.py revision
1.12 (which should be visible on the website in an hour or so),
http://cvs.biopython.org/cgi-bin/viewcvs/viewcvs.cgi/biopython/Bio/KEGG/Enzyme/__init__.py?cvsroot=biopython

You should be able to edit your Bio/KEGG/Enzyme/__init__.py file by
hand, or you could update it by downloading the new one from CVS.  Ask
for help if you need clearer instructions...

Let us know if you have any other problems with KEGG.

Thanks,

Peter
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a template for unittests in biopython

Hi people,
I have posted here:
- http://github.com/dalloliogm/bio-test-datasets-repository/blob/master/templates/biopython/biotest_template.py

a draft for a template for unittests in biopython. You can also refer
to it as bug 2749 (http://bugzilla.open-bio.org/show_bug.cgi?id=2749).

So, the idea is that if we have a template for test files, it will be
easier for new developers to write new tests and modules.
This one in particular makes use of nose, and it has some example of
global fixtures (the two setUpClass and tearDownAll methods).

What do you think about it?
Cheers..

--

-- 

My blog on bioinformatics (now in English): http://bioinfoblog.it

Re: [BioPython] Does anyone use EZRetrieve?

Peter wrote:
> On Thu, Nov 20, 2008 at 8:53 PM, Peter <biopython <at> maubp.freeserve.co.uk> wrote:
>   
>> On Thu, Nov 20, 2008 at 8:46 PM, Bruce Southey <bsouthey <at> gmail.com> wrote:
>>     
>>> Hi,
>>> Does anyone use EZRetrieve
>>> (http://siriusb.umdnj.edu:18080/EZRetrieve/single_r.jsp) ?
>>> This allows a user to retrieve a human, mouse or rat genome nucleic sequence
>>> based on an valid identifier.
>>>
>>> I think that most of the functionality of Bio.EZRetrieve is already present
>>> in Biopython and the genome sources appear to be 5 years old. For example,
>>> it uses LocusLink that was discontinued March 2005.
>>>
>>> If so could you please let me know?
>>>       
>> Actually - could you let the whole mailing list know?  ;)
>>
>> Given nature of the database and the limited functionality this python
>> code offers, if no-one is using Bio.EZRetrieve then it could be
>> considered for deprecation.
>>     
>
> I've seen no replies so I've marked Bio.EZRetrieve as obsolete in CVS
> (and therefore for Biopython 1.50), and unless anyone speaks up it
> will be deprecated in the release after that.
>
> I'm not sure that the EZRetrieve data is that out of date (they may
> have updated things since Bruce looked), but all the Bio.EZRetrieve

Re: [BioPython] Does anyone use EZRetrieve?

> Hi,
> I got nothing back from this nor for Bio.Affy and Bio.NMR (I tried a couple
> of emails) so I would suggest you also mark these as depreciated for
> Biopython 1.5.

I'm being pedantic/nit-picking, but the next release will be Biopython
1.50, (one, fifty) and then Biopython 1.51 (one, fifty one).  There
never was a Biopython 1.5 (one, five).

> The EZRetrieve help page still refers to 2003 releases.
> http://siriusb.umdnj.edu:18080/EZRetrieve/help.jsp

Anyway - maybe you are right, and we could deprecate Bio.EZRetrieve in
Biopython 1.50 (rather than just declaring it obsolete with the
intension of deprecating it in Biopython 1.51).

Peter
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Re: [BioPython] Does anyone use EZRetrieve?

Peter wrote:
>> Hi,
>> I got nothing back from this nor for Bio.Affy and Bio.NMR (I tried a couple
>> of emails) so I would suggest you also mark these as depreciated for
>> Biopython 1.5.
>>     
>
> I'm being pedantic/nit-picking, but the next release will be Biopython
> 1.50, (one, fifty) and then Biopython 1.51 (one, fifty one).  There
> never was a Biopython 1.5 (one, five).
>
>   
Thanks as it is critical to get the numbers right! Perhaps I am missing 
a Bio.__version__ (but interesting history of numbering) .
>> The EZRetrieve help page still refers to 2003 releases.
>> http://siriusb.umdnj.edu:18080/EZRetrieve/help.jsp
>>     
>
> Anyway - maybe you are right, and we could deprecate Bio.EZRetrieve in
> Biopython 1.50 (rather than just declaring it obsolete with the
> intension of deprecating it in Biopython 1.51).
>
> Peter
>   
I know we have had this discussion before but either option is agreeable 
to me for these modules.

Bruce
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