On Wed, Apr 29, 2009 at 3:07 PM, C. Titus Brown <c...@msu.edu> wrote: > > On Wed, Apr 29, 2009 at 11:03:12AM +0200, Giovanni Marco Dall'Olio wrote: > -> On Wed, Apr 29, 2009 at 10:45 AM, Giovanni Marco Dall'Olio > -> <dalloli...@gmail.com> wrote: > -> > Now it seems to be working under an http proxy... > -> > -> ok... I have put the changes on github: > -> - > http://github.com/dalloliogm/pygr/commit/53d9b08d36c095bc97131a0cd0ab2f27594eaa94 > -> > -> I have tried to run the pygr tests but it gives me an error: > -> $: cd pygr > -> $: python tests/runtest.py > -> ERROR pathfix.stop: unable to import extension module: cannot import > -> name cnestedlist > > do: > > % python setup.py build_ext -i
ok, I have done it.
Now, I think I should study the pygr's tutorial first :)
When I run the tests for pygrdata.py, I receive the error attached
(file 'error1.txt'). It hangs a lot on some of the tests, and then it
complains about a file called 'err1.tmp' which doesn't exist.
I think that more or less the problem with the http_proxy is resolved,
because I am able to do pygr.Data.dir('') and receive a list of
resources. However, if I try to download a resource, I get another
error related to XMLRPCSequenceDB.
Basically:
- I have downloaded pygr 0.7.1 from the google page ()
- I have copied the modified version of coordinator.py in pygr/coordinator.py
- I followed this tutorial:
http://code.google.com/p/pygr/wiki/PygrResourceDownloader
when I do:
>>> import os
>>> os.environ['PYGRDATAPATH'] = '.,http://biodb2.bioinformatics.ucla.edu:5000'
>>> import pygr.Data
it seems to work fine, it just prints some warnings I added.
then:
>>> os.environ['PYGRDATADOWNLOAD'] = '/my/seqdb/path'
>>> pygr.Data.dir('')
['Bio.MSA.UCSC.bosTau2ToBostau3',
'Bio.MSA.UCSC.bosTau3ToBostau4',
'Bio.MSA.UCSC.bosTau4_multiz5way',
'Bio.MSA.UCSC.calJac1_multiz9way',
'Bio.MSA.UCSC.canFam2_multiz4way',
'Bio.MSA.UCSC.ce2ToCe4',
'Bio.MSA.UCSC.danRer2ToDanrer3',
.... a long list of resources ...']
>>> m = pygr.Data.Bio.MSA.UCSC.bosTau2ToBostau3()
TypeError Traceback (most recent call last)
(see the second log file attached for details, pygr_XMLRPCSequenceDB.error)
TypeError: object.__new__(XMLRPCSequenceDB) is not safe, use dict.__new__()
> cheers,
> --titus
> --
> C. Titus Brown, c...@msu.edu
>
> >
>
--
Giovanni Dall'Olio, phd student
Department of Biologia Evolutiva at CEXS-UPF (Barcelona, Spain)
My blog on bioinformatics: http://bioinfoblog.it
--~--~---------~--~----~------------~-------~--~----~
You received this message because you are subscribed to the Google Groups
"pygr-dev" group.
To post to this group, send email to pygr-dev@googlegroups.com
To unsubscribe from this group, send email to
pygr-dev+unsubscr...@googlegroups.com
For more options, visit this group at
http://groups.google.com/group/pygr-dev?hl=en
-~----------~----~----~----~------~----~------~--~---
python protest.py
proxy.upf.es:8080
setting up http_proxy
http_proxy set
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . .Building sequence length index...
Index files saved.
Building index: formatdb -i "/tmp/tmp6hI2iv/sp_hbb1" -n
"/tmp/tmp6hI2iv/wikiwacky" -o T
WARNING: your query sequence is part of this database. Pygr alignments
normally do not report self-matches, i.e. the alignment of a sequence interval
to itself, so only homologies to OTHER sequences in the database
(or other intervals of the query sequence, if they are homologous) will be
reported (or an empty query result if no such homologies are found).
To report ALL homologies, including the self-match, simply create a new
sequence object and use that as your query, e.g.
query = sequence.Sequence(str(seq),"myquery")
results = db.blast(query)
To turn off this message, use the verbose=False option
Traceback (most recent call last):
File "protest.py", line 107, in <module>
if do_test(sys.argv[2],sys.argv[3],sys.argv[4]):
File "protest.py", line 21, in do_test
m()
File "/home/gioby/Local_Repository/pygr/tests/sequence_test.py", line 93, in
blast_test
assert approximate_cmp(result,correct,.0001)==0, 'blast results should
match'
AssertionError: blast results should match
. . . . . . . . . .Building sequence length index...
Index files saved.
. .
Traceback (most recent call last):
File "protest.py", line 110, in <module>
run_all_tests(find_tests(*(sys.argv[1:])))
File "protest.py", line 78, in run_all_tests
ifile = file(outfile)
IOError: [Errno 2] No such file or directory: 'err1.tmp'
pygr_XMLRPCSequenceDB.error
Description: Binary data
