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.
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.txtAnd 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_scriptself.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 mainFile "<frozen importlib._bootstrap>", line 1027, in _find_and_loadFile "<frozen importlib._bootstrap>", line 1002, in _find_and_load_unlockedFile "<frozen importlib._bootstrap>", line 945, in _find_specFile "<frozen importlib._bootstrap_external>", line 1439, in find_specFile "<frozen importlib._bootstrap_external>", line 1411, in _get_specFile "<frozen zipimport>", line 170, in find_specFile "<frozen importlib._bootstrap>", line 431, in spec_from_loaderFile "<frozen importlib._bootstrap_external>", line 741, in spec_from_file_locationFile "<frozen zipimport>", line 229, in get_filenameFile "<frozen zipimport>", line 767, in _get_module_codeFile "<frozen zipimport>", line 696, in _compile_sourceFile "/home/xxxx/mambaforge/lib/python3.10/site-packages/PEGASAS-1.1.1-py3.10.egg/PEGASAS/PEGASAS_pathway.py", line 101print 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.pyin the compiled filePEGASAS-1.1.1-py3.10.eggor if I need to install anything else.