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Description
Hi, in trying to run the example file (after have checked that the requirements are correctly installed) using the code that you show in your example guide:
PEGASAS pathway -o test example/geneExpbySample_example.txt PEGASAS/data/hallmarks50-2.gmt.txt example/groupInfo_example.txt
And it returns the next error:
/home/xxxx/mambaforge/bin/PEGASAS:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
__import__('pkg_resources').run_script('PEGASAS==1.1.1', 'PEGASAS')
Traceback (most recent call last):
File "/home/xxxx/mambaforge/bin/PEGASAS", line 4, in <module>
__import__('pkg_resources').run_script('PEGASAS==1.1.1', 'PEGASAS')
File "/home/xxxx/mambaforge/lib/python3.10/site-packages/pkg_resources/__init__.py", line 722, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/home/xxxx/mambaforge/lib/python3.10/site-packages/pkg_resources/__init__.py", line 1572, in run_script exec(script_code, namespace, namespace)
File "/home/xxxx/mambaforge/lib/python3.10/site-packages/PEGASAS-1.1.1-py3.10.egg/EGG-INFO/scripts/PEGASAS", line 80, in <module>
File "/home/xxxx/mambaforge/lib/python3.10/site-packages/PEGASAS-1.1.1-py3.10.egg/EGG-INFO/scripts/PEGASAS", line 23, in main
File "<frozen importlib._bootstrap>", line 1027, in _find_and_load
File "<frozen importlib._bootstrap>", line 1002, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 945, in _find_spec
File "<frozen importlib._bootstrap_external>", line 1439, in find_spec
File "<frozen importlib._bootstrap_external>", line 1411, in _get_spec
File "<frozen zipimport>", line 170, in find_spec
File "<frozen importlib._bootstrap>", line 431, in spec_from_loader
File "<frozen importlib._bootstrap_external>", line 741, in spec_from_file_location
File "<frozen zipimport>", line 229, in get_filename
File "<frozen zipimport>", line 767, in _get_module_code
File "<frozen zipimport>", line 696, in _compile_source
File "/home/xxxx/mambaforge/lib/python3.10/site-packages/PEGASAS-1.1.1-py3.10.egg/PEGASAS/PEGASAS_pathway.py", line 101
print gs
^^^^^^^^
SyntaxError: Missing parentheses in call to 'print'. Did you mean print(...)?
I'm new in bash and python so I don't know if I'm doing something wrong or the errors comes from the file named PEGASAS_pathway.py in the compiled file PEGASAS-1.1.1-py3.10.egg or if I need to install anything else.