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I have the following Orange Bioinformatics code.

#!/usr/bin/env python

from Orange.bio import arrayexpress
print arrayexpress.query_experiments(accession='E-MEXP-31')

But when I run it using Python 2.7.8, it shows up the following error.

Traceback (most recent call last):
  File "./main.py", line 4, in <module>
    print arrayexpress.query_experiments(accession='E-MEXP-31')
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/orangecontrib/bio/arrayexpress.py", line 354, in query_experiments
    return parse_json(io.TextIOWrapper(stream, ecoding="utf-8"))
TypeError: 'ecoding' is an invalid keyword argument for this function

Does anybody know how to fix the problem? Thanks.

Orange version

Orange-Bioinformatics version

Expected behavior

Actual behavior

running install_lib
copying _bioinformatics.py -> C:\Program Files (x86)\Orange\Lib\site-packages
error: [Errno 13] Permission denied: 'C:\Program Files (x86)\Orange\Lib\site-packages\_bioinformatics.py'

Steps to reproduce the behavior

Additional info (worksheets, data, screenshots, ...)

Hi,

I wanted to use some *.res files on Orange. It's similar to *.soft files but simpler, and it don't have anything like !subset_description to store class information. Nevertheless my code tries to extract classes from .res using simple regexes.

Please have a look on res2tab.py and tell me if you like useful, it's somewhat similar to your scripts/geo2orange.py

Hi !

I was really happy to see a nice OBO ontology parser for python in your package and think it can be very useful. Of course the first thing I did was use the to_networkx() method to manipulate and calculate things on the graph. But the conversion seems to leave out some essential information:

In [1]: from orangecontrib.bio.ontology import OBOOntology
In [2]: onto = OBOOntology('/Users/xapple/seqenv/data/envo.obo')
In [3]: nwrk = onto.to_networkx()
In [4]: nwrk.is_directed()
Out[4]: False

genesets = geneset.collections((("KEGG",), "Homo sapiens"))

I get many error messages that boil down to:

"requests.exceptions.ConnectionError: HTTPConnectionPool(host='asterix.fri.uni-lj.si', port=80): Max retries exceeded with url: /orngServerFiles/public/info (Caused by NewConnectionError('<requests.packages.urllib3.connection.HTTPConnection object at 0x10bf679b0>: Failed to establish a new connection: [Errno 8] nodename nor servname provided, or not known',))"

It seems that host='asterix.fri.uni-lj.si' doesn't exist. I was wondering if you could provide me with an updated link or point me in the right direct?

Thank you for your time

Aaron

Orange version

Orange-Bioinformatics version

Expected behavior

Actual behavior

Steps to reproduce the behavior

Additional info (worksheets, data, screenshots, ...)

Orange version

3.3.8

Orange-Bioinformatics version

2.6.19

Expected behavior

The widget should support selection of genes (rows).

Actual behavior

Widget often crashes after various types of selections.

Error encountered in widget Gene Info:

Traceback (most recent call last):
  File "/Applications/Orange3.app/Contents/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages/Orange/widgets/gui.py", line 2080, in do_commit
    commit()
  File "/Applications/Orange3.app/Contents/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages/orangecontrib/bio/widgets3/OWGeneInfo.py", line 577, in commit
    newdata[:, meta] = col_data
  File "/Applications/Orange3.app/Contents/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages/Orange/data/table.py", line 784, in __setitem__
    self.metas[row_idx, meta_cols] = value
ValueError: could not broadcast input array from shape (3) into shape (3,1)

Steps to reproduce the behavior

File->Data Table->Gene Info->Data Table, using brown-selected, where we have selected about ten rows in the first Data Table. Any selection in the Gene Info should then propagate the corresponding data rows to the second Data Table.

@ajdapretnar

In OWFeatureSelection.py

from .utils import gui as guiutils
from .utils import group as grouputils
from .utils.settings import SetContextHandler`

we don't need to do the relative path .utils because utils and python script are in the same directory.

I was getting an error while trying to import
Similar to this one : http://stackoverflow.com/questions/16637428/relative-import-in-python-3-not-working

instead it should be

from utils import gui as guiutils
from utils import group as grouputils
from utils.settings import SetContextHandler`

This needs to be solved before solving issue #71

version:
2.6.20

raised exception:
obiTaxonomy.UnknownSpeciesIdentifier

place:
bio/go.py line 782

problem:
serverfiles.ServerFiles().listfiles() was called before the exception
This returns a list of tuples (line 30 in serverfiles.py), e.g., [('GO', 'gene_as....tar.gz')]
This list was checked for 'filename' instead of a second tuple column list

Orange version

3.4.6-dev

Orange-Bioinformatics version

2.6.21

Expected behavior

KEGG Pathways widget works.

Actual behavior

KEGG is broken and doesn't work.

Steps to reproduce the behavior

Geo Datasets (G1210) - KEGG.

Additional info (worksheets, data, screenshots, ...)

Traceback (most recent call last):
File "/Users/ajda/orange/orange-bio/orangecontrib/bio/widgets3/OWKEGGPathwayBrowser.py", line 713, in _onEnrichTaskFinished
self._enrichTask.result()
File "/Users/ajda/orange/orange3/Orange/widgets/utils/concurrent.py", line 317, in result
return self._future.result(timeout)
File "/Users/ajda/anaconda/envs/o3/lib/python3.5/concurrent/futures/_base.py", line 398, in result
return self.__get_result()
File "/Users/ajda/anaconda/envs/o3/lib/python3.5/concurrent/futures/_base.py", line 357, in __get_result
raise self._exception
File "/Users/ajda/orange/orange3/Orange/widgets/utils/concurrent.py", line 327, in _execute
result = self.run()
File "/Users/ajda/orange/orange3/Orange/widgets/utils/concurrent.py", line 308, in run
return self.function()
File "/Users/ajda/orange/orange-bio/orangecontrib/bio/widgets3/OWKEGGPathwayBrowser.py", line 703, in
run_enrichment(org_code, genes, reference, progress)
File "/Users/ajda/orange/orange-bio/orangecontrib/bio/widgets3/OWKEGGPathwayBrowser.py", line 691, in run_enrichment
pathways.keys(), progress_callback=progress
File "/Users/ajda/orange/orange-bio/orangecontrib/bio/kegg/databases.py", line 239, in pre_cache
self.api.get(batch)
File "/Users/ajda/orange/orange-bio/orangecontrib/bio/kegg/caching.py", line 184, in call
rval = self.function(self.instance, *args)
File "/Users/ajda/orange/orange-bio/orangecontrib/bio/kegg/api.py", line 394, in get
return self._batch_get(ids)
File "/Users/ajda/orange/orange-bio/orangecontrib/bio/kegg/api.py", line 447, in _batch_get
entries = [store[key].value for key in keys]
File "/Users/ajda/orange/orange-bio/orangecontrib/bio/kegg/api.py", line 447, in
entries = [store[key].value for key in keys]
File "/Users/ajda/orange/orange-bio/orangecontrib/bio/kegg/caching.py", line 63, in getitem
raise KeyError(key)
KeyError: "get('path:hsa00300',)"

Bioinformatics Add-on often uses isnan to check for unknowns even in places, where one would expect string values. isnan fails for strings. Check whether these functions work and how. Fix the issue for empty strings accordingly.

Widgets that use isnan:

• OWFeatureSelection
• OWGeneInfo
• OWEnrichmentAnalysis
• OWKEGG
• OWSelectGenes