Print error of GOTerm class in obo_parser

[tanghaibao]

Print error of GOTerm class in obo_parser

[dvklopfenstein]

Thank you for your interest in GOATOOLS and taking the time to contact us.

In an old version of GOATOOLS, this issue could show up. Did you download GOATOOLS using 'pip install' or did you clone from the repo?

What version of GOATOOLS are you using? Do this to see the version:

$ python
Python 2.7.13 (default, Mar 13 2017, 20:56:15)
>>> import goatools
>>> print goatools.__version__
0.6.10

Also, try running this GOATOOLS test on your machine and let us know what you see:

$ cd <GOATOOLS_REPO>
$ python tests/test_go_print.py

[dvklopfenstein]

It looks like you may not be reading a go-basic.obo file. Try this code. You will need to have an "go-basic.obo" file downloaded from http://geneontology.org/ontology/go-basic.obo:

reader = OBOReader("go-basic.obo")
for rec in reader: print(rec)

[harryscholes]

When I opened the issue I was using the latest version 0.6.10 cloned from the Git repo with Python 3.6.0. I have also tried installing with pip, but that produces the same error. I also have the latest GO downloaded.

Running test_go_print.py outputs:

$ python tests/test_go_print.py
  EXISTS: go-basic.obo

<goatools.obo_parser.OBOReader object at 0x11050a908>

Traceback (most recent call last):
  File "tests/test_go_print.py", line 19, in <module>
    test_go_print()
  File "tests/test_go_print.py", line 14, in test_go_print
    prt.write("First GO Record: {REC}\n".format(REC=go_terms[0]))
  File "/Users/harry/anaconda/lib/python3.6/site-packages/goatools/obo_parser.py", line 260, in __str__
    NAME=self.name, NS=self.namespace, OLD=obsolete)
TypeError: unsupported format string passed to NoneType.__format__

Does this help in any way?

[dvklopfenstein]

Please do a pull request and re-run the test_go_print.py again. I added some more prints so that we may obtain more information. Please copy everything you see into your reply. Also, when you 'ls' on the obo file, what do you see. I see this:

$ ls -lrt go-basic.obo
-rw-r--r--+ 1 note2 note2 33520340 May 30 16:02 go-basic.obo

[harryscholes]

After pulling the new master and downloading the latest GO:

$ ls -l go-basic.obo
-rw-r--r--  1 harry  staff  33520340 May 29 14:33 go-basic.obo

Running test_go_print.py fails when iterating over the go_terms object:

$ python tests/test_go_print.py
  EXISTS: go-basic.obo

OBOReader: <goatools.obo_parser.OBOReader object at 0x10be4d470>

format-version: 1.2
data-version: releases/2017-05-28

Found 46645 GO Records:
Traceback (most recent call last):
  File "tests/test_go_print.py", line 21, in <module>
    test_go_print()
  File "tests/test_go_print.py", line 18, in test_go_print
    prt.write("{I:>7,} {RECORD}\n".format(I=idx, RECORD=go_rec))
  File "/Users/harry/anaconda/lib/python3.6/site-packages/goatools-0.6.10-py3.6.egg/goatools/obo_parser.py", line 260, in __str__
TypeError: unsupported format string passed to NoneType.__format__

[dvklopfenstein]

Okay thanks. Let me look into it...

[dvklopfenstein]

Please do a pull and re-run the test again. I changed the code so if the level and depth have not been initialized level and depth will not print.

[harryscholes]

Pulled and re-run, but it's still trying to format None into strings:

$ python tests/test_go_print.py
  EXISTS: go-basic.obo
Python Version: 3.6.0 |Anaconda custom (x86_64)| (default, Dec 23 2016, 13:19:00)
[GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.57)]


OBOReader: <goatools.obo_parser.OBOReader object at 0x1058fd438>

format-version: 1.2
data-version: releases/2017-05-28

Found 46645 GO Records:
Traceback (most recent call last):
  File "tests/test_go_print.py", line 22, in <module>
    test_go_print()
  File "tests/test_go_print.py", line 19, in test_go_print
    prt.write("{I:>7,} {RECORD}\n".format(I=idx, RECORD=go_rec))
  File "/Users/harry/anaconda/lib/python3.6/site-packages/goatools-0.6.10-py3.6.egg/goatools/obo_parser.py", line 260, in __str__
TypeError: unsupported format string passed to NoneType.__format__

Do you see this error as well?

[dvklopfenstein]

Thanks for re-running it. I am not seeing this error, but my daily work is done with Python 2.7. I see that you are using Python 3.6. I will try that version of Python to re-create what you are seeing.

[dvklopfenstein]

I am still working on it and will get back to you soon.

[dvklopfenstein]

I am taking a look at this issue now. Thank you for your patience. I had a work deadline, which took me away from your issue.

[dvklopfenstein]

I just ran the script using python3 and was not able to replicate the error you are seeing. This is what I did:

 $ python3 tests/test_go_print.py

[dvklopfenstein]

@tanghaibao , can you please create a new PyPI version of goatools?

goatools-0.6.10.tar.gz (md5) available from https://pypi.python.org/pypi/goatools was uploaded on 2016-10-06. There have been many updates since then. It would likely be helpful to create a new snapshot for PyPI.

Issue #61 was corrected May19, 2016, so this may not be it. But there have been significant updates to GOATOOLS since 2016-10-06.

[dvklopfenstein]

@harryscholes , Can you try setting your PYTHONPATH such that your cloned copy of the goatools repo is near the beginning? It might look like this:

export PYTHONPATH=.:/Users/harry/git/goatools

And then re-run?:

python3 tests/test_go_print.py

[harryscholes]

Hi,

I just created a clean conda env to test all this:

What works:

• Cloning the git repo + adding the repo path to $PYTHONPATH

conda create -n goatest python=3
source activate goatest
cd ~/git
git clone [email protected]:tanghaibao/goatools.git
export PYTHONPATH=.:/Users/harry/git/goatools
python goatools/tests/test_go_print.py

• pip installing the git repo

conda create -n goatest python=3
source activate goatest
pip install git+https://github.com/tanghaibao/goatools
python goatools/tests/test_go_print.py

What doesn't work:

• pip installing the PyPI version

conda create -n goatest python=3
source activate goatest
pip install goatools
python goatools/tests/test_go_print.py  # produces same error as before

  EXISTS: go-basic.obo
Python Version: 3.6.1 |Continuum Analytics, Inc.| (default, May 11 2017, 13:04:09)
[GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.57)]


OBOReader: <goatools.obo_parser.OBOReader object at 0x10ad029e8>

format-version: 1.2
data-version: releases/2017-06-14

Found 46825 GO Records:
Traceback (most recent call last):
  File "tests/test_go_print.py", line 22, in <module>
    test_go_print()
  File "tests/test_go_print.py", line 19, in test_go_print
    prt.write("{I:>7,} {RECORD}\n".format(I=idx, RECORD=go_rec))
  File "/Users/harry/anaconda3/envs/goa/lib/python3.6/site-packages/goatools/obo_parser.py", line 260, in __str__
    NAME=self.name, NS=self.namespace, OLD=obsolete)
TypeError: unsupported format string passed to NoneType.__format__

Looks like we're getting somewhere 👍

[dvklopfenstein]

Thank you for trying all those options and reporting back.

We just released a new version for PyPI this week. The new version is goatools-0.7.9

Please let us know if this new version works for you when you get a chance. Thank you for your interest in GOATOOLS and taking the time to report this issue.

[harryscholes]

Latest PyPI and git GOATOOLS:

conda create -n goatest python=3
source activate goatest
pip install goatools
cd git
git clone [email protected]:tanghaibao/goatools.git
python goatools/tests/test_go_print.py

Traceback (most recent call last):
  File "goatools/tests/test_go_print.py", line 34, in <module>
    test_go_print()
  File "goatools/tests/test_go_print.py", line 11, in test_go_print
    prt_pypath(prt)
  File "goatools/tests/test_go_print.py", line 25, in prt_pypath
    pypathes = os.environ['PYTHONPATH']
  File "/Users/harry/anaconda3/envs/goatest/lib/python3.6/os.py", line 669, in __getitem__
    raise KeyError(key) from None
KeyError: 'PYTHONPATH'

NB this method does not create a $PYTHONPATH. If I comment out line 11 in test_go_print.py: # prt_pypath(prt) then all works well.

[dvklopfenstein]

Thank you for checking that out. I am so glad that it works for you. I've updated the test to fix the issue you mention in your last comment regarding PYTHONPATH.

Thank you for your interest in GOATOOLS and taking the time to report the issue.

I am closing this issue now. Please contact us if needed in the future.

[harryscholes]

Great! Keep up the good work with GOATOOLS 😄