pairwise is not working even on --test #40

unique379 · 2020-09-15T16:07:59Z

Hi
install latest version of intervene using git but its not working for pairwise. and by the way, using conda, its installing 0.5.8 which is not latest and does not work either for pairwise.

intervene pairwise --test

Running Intervene with test data.


Performing a pairwise intersection analysis. Please wait...

Traceback (most recent call last):
  File "/Users/rupeshk/miniconda3/bin/intervene", line 4, in <module>
    __import__('pkg_resources').run_script('intervene==0.6.4', 'intervene')
  File "/Users/rupeshk/miniconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 665, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/Users/rupeshk/miniconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1463, in run_script
    exec(code, namespace, namespace)
  File "/Users/rupeshk/miniconda3/lib/python3.7/site-packages/intervene-0.6.4-py3.7.egg/EGG-INFO/scripts/intervene", line 606, in <module>
    main()
  File "/Users/rupeshk/miniconda3/lib/python3.7/site-packages/intervene-0.6.4-py3.7.egg/EGG-INFO/scripts/intervene", line 426, in main
    pairwise.pairwise_intersection(label_names, options)
  File "/Users/rupeshk/miniconda3/lib/python3.7/site-packages/intervene-0.6.4-py3.7.egg/intervene/modules/pairwise/pairwise.py", line 480, in pairwise_intersection
    barplot(series, matrix, outfile, options, max_size=max(bed_sizes))
  File "/Users/rupeshk/miniconda3/lib/python3.7/site-packages/intervene-0.6.4-py3.7.egg/intervene/modules/pairwise/pairwise.py", line 135, in barplot
    cax, order = heatmap_triangle(matrix, ax, options)
  File "/Users/rupeshk/miniconda3/lib/python3.7/site-packages/intervene-0.6.4-py3.7.egg/intervene/modules/pairwise/pairwise.py", line 214, in heatmap_triangle
    D = D.ix[cluster_order, cluster_order]
  File "/Users/rupeshk/miniconda3/lib/python3.7/site-packages/pandas/core/generic.py", line 5274, in __getattr__
    return object.__getattribute__(self, name)
AttributeError: 'DataFrame' object has no attribute 'ix'

The text was updated successfully, but these errors were encountered:

bioinfouser · 2020-10-07T13:59:34Z

I am not the owner of intervene, but it works with python 2.7. Just make a new conda environment and reinstall. It should run

zhypan · 2020-10-09T00:18:42Z

DId you fix it? I meet some problem when used the intervene pairwise --htype tribar

asntech · 2020-10-12T19:57:49Z

Hi @unique379 @zhypan. It is fixed now. Please try to install it from the source.

bernt-matthias · 2020-11-09T15:50:43Z

Just to be sure: this is not fixed in the latest release (0.6.4)? Asking because I just fixed the conda package (by requiring pandas <1.0) .. see bioconda/bioconda-recipes#25235

asntech · 2020-11-17T01:44:30Z

sorry, this was not pushed to pypi. Please try now with v0.6.5.
conda install -c bioconda intervene==0.6.5

bernt-matthias · 2020-11-17T09:02:48Z

Thanks a lot, this means that I can remove the restriction pandas<1 from the conda recipe, right?

- remove/invert restriction on pandas which was fixed in 0.6.5 asntech/intervene#40 (comment) - running the tool outputs deprection warnings for matplotlib >= 3.4 .. so I added a version restriction

Merge PR #25392, commits were: * remove create test data (as workaround) for ``` Traceback (most recent call last): File "/home/circleci/project/miniconda/bin/bioconda-utils", line 8, in <module> sys.exit(main()) File "/home/circleci/project/miniconda/lib/python3.7/site-packages/bioconda_utils/cli.py", line 971, in main bioconductor_skeleton, clean_cran_skeleton, autobump, bot File "/home/circleci/project/miniconda/lib/python3.7/site-packages/argh/dispatching.py", line 328, in dispatch_commands dispatch(parser, *args, **kwargs) File "/home/circleci/project/miniconda/lib/python3.7/site-packages/argh/dispatching.py", line 174, in dispatch for line in lines: File "/home/circleci/project/miniconda/lib/python3.7/site-packages/argh/dispatching.py", line 277, in _execute_command for line in result: File "/home/circleci/project/miniconda/lib/python3.7/site-packages/argh/dispatching.py", line 260, in _call result = function(*positional, **keywords) File "<boltons.funcutils.FunctionBuilder-5>", line 2, in build File "/home/circleci/project/miniconda/lib/python3.7/site-packages/bioconda_utils/cli.py", line 130, in wrapper func(*args, **kwargs) File "<boltons.funcutils.FunctionBuilder-4>", line 2, in build File "/home/circleci/project/miniconda/lib/python3.7/site-packages/bioconda_utils/cli.py", line 59, in wrapper func(*args, **kwargs) File "/home/circleci/project/miniconda/lib/python3.7/site-packages/bioconda_utils/cli.py", line 476, in build keep_old_work=keep_old_work) File "/home/circleci/project/miniconda/lib/python3.7/site-packages/bioconda_utils/build.py", line 343, in build_recipes linter=linter) File "/home/circleci/project/miniconda/lib/python3.7/site-packages/bioconda_utils/build.py", line 149, in build pkg_test.test_package(pkg_path, base_image=base_image) File "/home/circleci/project/miniconda/lib/python3.7/site-packages/bioconda_utils/pkg_test.py", line 170, in test_package p = utils.run(cmd, env=env, cwd=d, mask=False) File "/home/circleci/project/miniconda/lib/python3.7/tempfile.py", line 805, in __exit__ self.cleanup() File "/home/circleci/project/miniconda/lib/python3.7/tempfile.py", line 809, in cleanup _shutil.rmtree(self.name) File "/home/circleci/project/miniconda/lib/python3.7/shutil.py", line 485, in rmtree _rmtree_safe_fd(fd, path, onerror) File "/home/circleci/project/miniconda/lib/python3.7/shutil.py", line 423, in _rmtree_safe_fd _rmtree_safe_fd(dirfd, fullname, onerror) File "/home/circleci/project/miniconda/lib/python3.7/shutil.py", line 443, in _rmtree_safe_fd onerror(os.unlink, fullname, sys.exc_info()) File "/home/circleci/project/miniconda/lib/python3.7/shutil.py", line 441, in _rmtree_safe_fd os.unlink(entry.name, dir_fd=topfd) PermissionError: [Errno 13] Permission denied: 'Intervene_pairwise_frac_matrix.txt' ``` * add proper tests to intervene - remove/invert restriction on pandas which was fixed in 0.6.5 asntech/intervene#40 (comment) - running the tool outputs deprection warnings for matplotlib >= 3.4 .. so I added a version restriction

asntech · 2020-12-02T10:30:27Z

Thanks @bernt-matthias !!

allenyen · 2022-07-23T01:32:34Z

Hi, I am having trouble with getting pairwise to run with --test as well. I created a conda env using conda create -n intervene python=3.6 intervene=0.6.5. Venn and upset work with --test, however I get the following when trying it with pairwise.

intervene pairwise --test

Running Intervene with test data.


Performing a pairwise intersection analysis. Please wait...

Traceback (most recent call last):
  File "/home/a.yen/miniconda3/envs/intervene/bin/intervene", line 604, in <module>
    main()
  File "/home/a.yen/miniconda3/envs/intervene/bin/intervene", line 424, in main
    pairwise.pairwise_intersection(label_names, options)
  File "/home/a.yen/miniconda3/envs/intervene/lib/python3.6/site-packages/intervene/modules/pairwise/pairwise.py", line 464, in pairwise_intersection
    matrix = pd.read_table(matrix_file,index_col=0, delim_whitespace=True)
  File "/home/a.yen/.local/lib/python3.6/site-packages/pandas/io/parsers.py", line 755, in read_table
    return read_csv(**locals())
  File "/home/a.yen/.local/lib/python3.6/site-packages/pandas/io/parsers.py", line 625, in read_csv
    "Specified a delimiter with both sep and "
ValueError: Specified a delimiter with both sep and delim_whitespace=True; you can only specify one.

asntech · 2022-07-24T06:49:37Z

@allenyen can you check the pandas version installed? And please try to update pandas with v1.2.x
pandas-dev/pandas#36560

allenyen · 2022-07-24T23:02:14Z

I couldn't get pandas >1.1.5 with python3.6, so I created an entirely new environment with python 3.9 and pandas 1.4.3 and it works now. Thanks!

yulijia mentioned this issue Oct 9, 2020

After upgrade to pandas 1.0.0, DataFrame.ix is removed #37

Closed

asntech added a commit that referenced this issue Oct 12, 2020

fixed for pandas v1.0.0 #37 #40

c447413

bernt-matthias mentioned this issue Nov 17, 2020

add proper tests to intervene bioconda/bioconda-recipes#25392

Merged

asntech closed this as completed Jul 14, 2023

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

pairwise is not working even on --test #40

pairwise is not working even on --test #40

unique379 commented Sep 15, 2020 •

edited

Loading

bioinfouser commented Oct 7, 2020

zhypan commented Oct 9, 2020

asntech commented Oct 12, 2020

bernt-matthias commented Nov 9, 2020

asntech commented Nov 17, 2020

bernt-matthias commented Nov 17, 2020

asntech commented Dec 2, 2020

allenyen commented Jul 23, 2022

asntech commented Jul 24, 2022

allenyen commented Jul 24, 2022

pairwise is not working even on --test #40

pairwise is not working even on --test #40

Comments

unique379 commented Sep 15, 2020 • edited Loading

bioinfouser commented Oct 7, 2020

zhypan commented Oct 9, 2020

asntech commented Oct 12, 2020

bernt-matthias commented Nov 9, 2020

asntech commented Nov 17, 2020

bernt-matthias commented Nov 17, 2020

asntech commented Dec 2, 2020

allenyen commented Jul 23, 2022

asntech commented Jul 24, 2022

allenyen commented Jul 24, 2022

unique379 commented Sep 15, 2020 •

edited

Loading