dvklopfenstein
commented
4 years ago Hello,
Thank you for your interest in GOATOOLS and taking the time to write us.
Could you give Python3 a try?
python3 scripts/find_enrichment.py --pval=0.05 --indent data/study.txt data/population.txt data/association.txt --outfile=goea_results.tsvWhat operating system are you using?
uname -a
What version of Python are you using?
$ python --version
Python 3.6.9What is the version of some of the Python packages that you are using?
$ python3
Python 3.6.9 (default, Jul 21 2019, 14:33:59)
[GCC 7.4.0] on cygwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy
>>> print(numpy.version.version)
1.16.2
>>> import statsmodels
>>> print(statsmodels.version.version)
0.9.0
>>> import pandas
>>> print(pandas.version.version)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
AttributeError: module 'pandas' has no attribute 'version'
>>> print(pandas.__version__)
0.22.0
>>> import goatools
>>> print(goatools.version.version)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
AttributeError: module 'goatools' has no attribute 'version'
>>> print(goatools.__version__)
v0.9.9+80.gf08732d
gosalone
Hi dear colleagues, I installed and run goatools with the test data and I got the error below.
$ python scripts/find_enrichment.py --pval=0.05 --indent data/study.txt data/population.txt data/association.txt --outfile=goea_results.tsv
go-basic.obo: fmt(1.2) rel(2020-02-21) 47,245 GO Terms HMS:0:00:00.703169 128,975 annotations READ: data/association.txt Study: 276 vs. Population 33239
Load BP Gene Ontology Analysis ... Propagating term counts up: is_a 87% 28,991 of 33,239 population items found in association
Load CC Gene Ontology Analysis ... Propagating term counts up: is_a 86% 28,574 of 33,239 population items found in association
Load MF Gene Ontology Analysis ... Propagating term counts up: is_a 87% 28,910 of 33,239 population items found in association
Run BP Gene Ontology Analysis: current study set of 276 IDs ... 86% 237 of 276 study items found in association 100% 276 of 276 study items found in population(33239) Calculating 3,478 uncorrected p-values using fisher 3,478 GO terms are associated with 28,991 of 33,239 population items 461 GO terms are associated with 237 of 276 study items METHOD bonferroni: 3 GO terms found significant (< 0.05=alpha) ( 3 enriched + 0 purified): local bonferroni 33 study items associated with significant GO IDs (enriched) 0 study items associated with significant GO IDs (purified) METHOD sidak: 3 GO terms found significant (< 0.05=alpha) ( 3 enriched + 0 purified): local sidak 33 study items associated with significant GO IDs (enriched) 0 study items associated with significant GO IDs (purified) METHOD holm: 3 GO terms found significant (< 0.05=alpha) ( 3 enriched + 0 purified): local holm 33 study items associated with significant GO IDs (enriched) 0 study items associated with significant GO IDs (purified) Traceback (most recent call last): File "scripts/find_enrichment.py", line 44, in
main()
File "scripts/find_enrichment.py", line 31, in main
obj = GoeaCliFnc(GoeaCliArgs().args)
File "/home/tarek/.local/lib/python2.7/site-packages/goatools/cli/find_enrichment.py", line 233, in init
self.results_all = self.objgoeans.run_study(_study)
File "/home/tarek/.local/lib/python2.7/site-packages/goatools/goea/go_enrichment_ns.py", line 20, in run_study
ns2results = {ns:o.run_study(study_ids) for ns, o in sorted(self.ns2objgoea.items())}
File "/home/tarek/.local/lib/python2.7/site-packages/goatools/goea/go_enrichment_ns.py", line 20, in
ns2results = {ns:o.run_study(study_ids) for ns, o in sorted(self.ns2objgoea.items())}
File "/home/tarek/.local/lib/python2.7/site-packages/goatools/go_enrichment.py", line 312, in run_study
self._run_multitest_corr(results, methods, alpha, study, log)
File "/home/tarek/.local/lib/python2.7/site-packages/goatools/go_enrichment.py", line 395, in _run_multitest_corr
self._run_multitestnt_method.source
File "/home/tarek/.local/lib/python2.7/site-packages/goatools/go_enrichment.py", line 427, in _run_multitest_statsmodels
multipletests = self.methods.get_statsmodels_multipletests()
File "/home/tarek/.local/lib/python2.7/site-packages/goatools/multiple_testing.py", line 142, in get_statsmodels_multipletests
from statsmodels.sandbox.stats.multicomp import multipletests
File "/home/tarek/.local/lib/python2.7/site-packages/statsmodels/sandbox/init.py", line 4, in
from statsmodels.tools._testing import PytestTester
File "/home/tarek/.local/lib/python2.7/site-packages/statsmodels/tools/init.py", line 1, in
from .tools import add_constant, categorical
File "/home/tarek/.local/lib/python2.7/site-packages/statsmodels/tools/tools.py", line 8, in
from statsmodels.compat.python import lzip, lmap
File "/home/tarek/.local/lib/python2.7/site-packages/statsmodels/compat/init.py", line 1, in
from statsmodels.tools._testing import PytestTester
File "/home/tarek/.local/lib/python2.7/site-packages/statsmodels/tools/_testing.py", line 11, in
from statsmodels.compat.pandas import assert_equal
File "/home/tarek/.local/lib/python2.7/site-packages/statsmodels/compat/pandas.py", line 4, in
import numpy as np
File "/home/tarek/.local/lib/python2.7/site-packages/statsmodels/compat/numpy.py", line 46, in
NP_LT_114 = LooseVersion(np.version) < LooseVersion('1.14')
AttributeError: 'module' object has no attribute 'version'
Could help me solve this problem. Thank you