2

I am trying to install pysam and pybedtools modules on python 3.4. But I got an Error: 

Collecting pysam
  Using cached pysam-0.9.0.tar.gz
    Complete output from command python setup.py egg_info:
    '.' is not recognized as an internal or external command,
    operable program or batch file.
    # pysam: htslib mode is shared
    # pysam: htslib configure options: None
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "C:\Users\ikirov.CLO\AppData\Local\Temp\pip-build-_me_xeme\pysam\setup.py", line 212, in <module>
        sys.abiflags)]
    AttributeError: 'module' object has no attribute 'abiflags'

Could you please help me with it?

IlGala
  • 3,331
  • 4
  • 35
  • 49
tov_Kirov
  • 21
  • 5

1 Answers1

0

Hi I got the same error last year during one of my class.

As I know back then, pysam simply won't work with python3 + windows environment. See this: https://github.com/pysam-developers/pysam/issues/353 looks like it is still unsolved now.

For my homework, I just used this http://bow.codeplex.com/

And my suggestion, just try to use linux or get a python2. Yes I know the scientific field is the slowest for the 2->3 transition. It sucks.

Yitong Ma
  • 51
  • 2