Entering edit mode
23 months ago
a.basitkhan1990
▴
60
Hello!
I am new to python (first time)
I am trying to use this on my MAF data: https://github.com/wangc29/MSIpred
I attempt to run the first line and get error:
(base) abkhan@Abduls-MacBook-Pro MSIpred-master % python2 setup.py install
running install
running bdist_egg
running egg_info
writing requirements to MSIpred.egg-info/requires.txt
writing MSIpred.egg-info/PKG-INFO
writing top-level names to MSIpred.egg-info/top_level.txt
writing dependency_links to MSIpred.egg-info/dependency_links.txt
reading manifest file 'MSIpred.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'MSIpred.egg-info/SOURCES.txt'
installing library code to build/bdist.macosx-10.9-x86_64/egg
running install_lib
running build_py
creating build/bdist.macosx-10.9-x86_64/egg
copying build/lib/.DS_Store -> build/bdist.macosx-10.9-x86_64/egg
creating build/bdist.macosx-10.9-x86_64/egg/MSIpred
copying build/lib/MSIpred/best_svm_pipeline.pkl -> build/bdist.macosx-10.9-x86_64/egg/MSIpred
copying build/lib/MSIpred/model_training.py -> build/bdist.macosx-10.9-x86_64/egg/MSIpred
copying build/lib/MSIpred/predict_msi.py -> build/bdist.macosx-10.9-x86_64/egg/MSIpred
copying build/lib/MSIpred/__init__.py -> build/bdist.macosx-10.9-x86_64/egg/MSIpred
copying build/lib/MSIpred/tagged_maf.py -> build/bdist.macosx-10.9-x86_64/egg/MSIpred
copying build/lib/MSIpred/raw_maf.py -> build/bdist.macosx-10.9-x86_64/egg/MSIpred
byte-compiling build/bdist.macosx-10.9-x86_64/egg/MSIpred/model_training.py to model_training.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/MSIpred/predict_msi.py to predict_msi.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/MSIpred/__init__.py to __init__.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/MSIpred/tagged_maf.py to tagged_maf.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/MSIpred/raw_maf.py to raw_maf.pyc
creating build/bdist.macosx-10.9-x86_64/egg/EGG-INFO
copying MSIpred.egg-info/PKG-INFO -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFO
copying MSIpred.egg-info/SOURCES.txt -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFO
copying MSIpred.egg-info/dependency_links.txt -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFO
copying MSIpred.egg-info/not-zip-safe -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFO
copying MSIpred.egg-info/requires.txt -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFO
copying MSIpred.egg-info/top_level.txt -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFO
creating 'dist/MSIpred-0.1-py2.7.egg' and adding 'build/bdist.macosx-10.9-x86_64/egg' to it
removing 'build/bdist.macosx-10.9-x86_64/egg' (and everything under it)
Processing MSIpred-0.1-py2.7.egg
removing '/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/MSIpred-0.1-py2.7.egg' (and everything under it)
creating /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/MSIpred-0.1-py2.7.egg
Extracting MSIpred-0.1-py2.7.egg to /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages
MSIpred 0.1 is already the active version in easy-install.pth
Installed /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/MSIpred-0.1-py2.7.egg
Processing dependencies for MSIpred==0.1
Searching for pandas
Reading https://pypi.org/simple/pandas/
Downloading https://files.pythonhosted.org/packages/4d/07/c4d69e1acb7723ca49d24fc60a89aa07a914dfb8e7a07fdbb9d8646630cd/pandas-1.5.2.tar.gz#sha256=220b98d15cee0b2cd839a6358bd1f273d0356bf964c1a1aeb32d47db0215488b
Best match: pandas 1.5.2
Processing pandas-1.5.2.tar.gz
Writing /var/folders/dj/d01g66_j455dnpmrtjd543qm0000gn/T/easy_install-gHzy5J/pandas-1.5.2/setup.cfg
Running pandas-1.5.2/setup.py -q bdist_egg --dist-dir /var/folders/dj/d01g66_j455dnpmrtjd543qm0000gn/T/easy_install-gHzy5J/pandas-1.5.2/egg-dist-tmp-olLtp6
Traceback (most recent call last):
File "setup.py", line 18, in <module>
zip_safe=False)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/setuptools/__init__.py", line 145, in setup
return distutils.core.setup(**attrs)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/core.py", line 151, in setup
dist.run_commands()
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py", line 953, in run_commands
self.run_command(cmd)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py", line 972, in run_command
cmd_obj.run()
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/setuptools/command/install.py", line 67, in run
self.do_egg_install()
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/setuptools/command/install.py", line 117, in do_egg_install
cmd.run()
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 418, in run
self.easy_install(spec, not self.no_deps)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 660, in easy_install
return self.install_item(None, spec, tmpdir, deps, True)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 707, in install_item
self.process_distribution(spec, dist, deps)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 752, in process_distribution
[requirement], self.local_index, self.easy_install
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pkg_resources/__init__.py", line 782, in resolve
replace_conflicting=replace_conflicting
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1065, in best_match
return self.obtain(req, installer)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1077, in obtain
return installer(requirement)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 679, in easy_install
return self.install_item(spec, dist.location, tmpdir, deps)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 705, in install_item
dists = self.install_eggs(spec, download, tmpdir)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 890, in install_eggs
return self.build_and_install(setup_script, setup_base)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 1158, in build_and_install
self.run_setup(setup_script, setup_base, args)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 1144, in run_setup
run_setup(setup_script, args)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/setuptools/sandbox.py", line 253, in run_setup
raise
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/contextlib.py", line 35, in __exit__
self.gen.throw(type, value, traceback)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/setuptools/sandbox.py", line 195, in setup_context
yield
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/contextlib.py", line 35, in __exit__
self.gen.throw(type, value, traceback)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/setuptools/sandbox.py", line 166, in save_modules
saved_exc.resume()
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/setuptools/sandbox.py", line 141, in resume
six.reraise(type, exc, self._tb)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/setuptools/sandbox.py", line 154, in save_modules
yield saved
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/setuptools/sandbox.py", line 195, in setup_context
yield
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/setuptools/sandbox.py", line 250, in run_setup
_execfile(setup_script, ns)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/setuptools/sandbox.py", line 44, in _execfile
code = compile(script, filename, 'exec')
File "/var/folders/dj/d01g66_j455dnpmrtjd543qm0000gn/T/easy_install-gHzy5J/pandas-1.5.2/setup.py", line 250
f"{extension}-source file '{sourcefile}' not found.\n"
^
SyntaxError: invalid syntax
(base) abkhan@Abduls-MacBook-Pro MSIpred-master %
Please advise?
