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yarden / MISO

MISO: Mixture of Isoforms model for RNA-Seq isoform quantitation
http://genes.mit.edu/burgelab/miso/index.html
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import pysplicing #136

Open MurliNair opened 5 years ago

MurliNair commented 5 years ago

Hi, I just installed misopy using pip. I was testing it by trying to import misopy and pysplicing, import misopy works fine, but pysplicing is giving the following error.

import misopy import pysplicing Traceback (most recent call last): File "", line 1, in File "/usr/local/lib64/python3.6/site-packages/pysplicing/init.py", line 2 MISO_START_AUTO=0L ^ SyntaxError: invalid syntax

Thanks for your help. Cheers../Murli

MurliNair commented 5 years ago

I tried reinstalling it and it still gives me an error. Tue May 28, 10:54:05 [root@genomics ~]# pip --version pip 19.1.1 from /usr/local/lib/python3.6/site-packages/pip (python 3.6)

Tue May 28, 10:56:26 [root@genomics ~]# pip install misopy Collecting misopy Using cached https://files.pythonhosted.org/packages/1e/1c/1ee24b5ed82b1c3b673345ecfc5e7a505273cfe5b450d6fc05479f1ad641/misopy-0.5.4.tar.gz Requirement already satisfied: matplotlib in /usr/local/lib64/python3.6/site-packages (from misopy) (3.1.0) Requirement already satisfied: numpy>=1.5.0 in /usr/local/lib64/python3.6/site-packages (from misopy) (1.16.3) Requirement already satisfied: scipy>=0.9.0 in /usr/local/lib64/python3.6/site-packages (from misopy) (1.3.0) Requirement already satisfied: pysam>=0.6.0 in /usr/local/lib64/python3.6/site-packages (from misopy) (0.15.2) Requirement already satisfied: kiwisolver>=1.0.1 in /usr/local/lib64/python3.6/site-packages (from matplotlib->misopy) (1.1.0) Requirement already satisfied: python-dateutil>=2.1 in /usr/local/lib/python3.6/site-packages (from matplotlib->misopy) (2.8.0) Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.6/site-packages (from matplotlib->misopy) (2.4.0) Requirement already satisfied: cycler>=0.10 in /usr/local/lib/python3.6/site-packages (from matplotlib->misopy) (0.10.0) Requirement already satisfied: setuptools in /usr/local/lib/python3.6/site-packages (from kiwisolver>=1.0.1->matplotlib->misopy) (40.6.2) Requirement already satisfied: six>=1.5 in /usr/local/lib/python3.6/site-packages (from python-dateutil>=2.1->matplotlib->misopy) (1.12.0) Installing collected packages: misopy Running setup.py install for misopy ... done Successfully installed misopy-0.5.4

Tue May 28, 11:02:17 [root@genomics ~]# python3 Python 3.6.8 (default, Apr 25 2019, 21:02:35) [GCC 4.8.5 20150623 (Red Hat 4.8.5-36)] on linux Type "help", "copyright", "credits" or "license" for more information.

import misopy import pysplicing Traceback (most recent call last): File "", line 1, in File "/usr/local/lib64/python3.6/site-packages/pysplicing/init.py", line 2 MISO_START_AUTO=0L ^ SyntaxError: invalid syntax

======================= Tue May 28, 11:54:45 [root@genomics ~/Downloads/test]# python3 -m unittest discover misopy -v misopy.test_cluster (unittest.loader._FailedTest) ... ERROR misopy.test_miso (unittest.loader._FailedTest) ... ERROR

====================================================================== ERROR: misopy.test_cluster (unittest.loader._FailedTest)

ImportError: Failed to import test module: misopy.test_cluster Traceback (most recent call last): File "/usr/lib64/python3.6/unittest/loader.py", line 428, in _find_test_path module = self._get_module_from_name(name) File "/usr/lib64/python3.6/unittest/loader.py", line 369, in _get_module_from_name import(name) File "/usr/local/lib64/python3.6/site-packages/misopy/test_cluster.py", line 30 print "Testing single-end SE event interface..." ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print("Testing single-end SE event interface...")?

====================================================================== ERROR: misopy.test_miso (unittest.loader._FailedTest)

ImportError: Failed to import test module: misopy.test_miso Traceback (most recent call last): File "/usr/lib64/python3.6/unittest/loader.py", line 428, in _find_test_path module = self._get_module_from_name(name) File "/usr/lib64/python3.6/unittest/loader.py", line 369, in _get_module_from_name import(name) File "/usr/local/lib64/python3.6/site-packages/misopy/test_miso.py", line 39 print "Testing conversion of SAM to BAM..." ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print("Testing conversion of SAM to BAM...")?

Ran 2 tests in 0.000s

FAILED (errors=2)

hua-2019-git commented 4 years ago

Hi, i am also meet the same question, pysplicing is giving the following error. import pysplicing Traceback (most recent call last): File "", line 1, in File "/usr/local/lib64/python3.6/site-packages/pysplicing/init.py", line 2 MISO_START_AUTO=0L ^ SyntaxError: invalid syntax

I'd like to know how you solved this problem. Thank you very much

obenno commented 4 years ago

Hi, I think the package was written by python2, maybe you should try python2.7.

ttran2020 commented 3 years ago

Hi, I just installed misopy using pip. I was testing it by trying to import misopy and pysplicing, import misopy works fine, but pysplicing is giving the following error.

import misopy import pysplicing Traceback (most recent call last): File "", line 1, in File "/usr/local/lib64/python3.6/site-packages/pysplicing/init.py", line 2 MISO_START_AUTO=0L ^ SyntaxError: invalid syntax

Thanks for your help. Cheers../Murli

Murli - Did you have a chance to address the issues? If yes, I would appreciate it if you can share. I got the same issue. Thanks. T

mbradyneeley commented 3 years ago

I encountered the same issue and like obenno commented using python2 instead of python3, import pysplicing was succesful.