Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Pysam #13

Closed
dalessandra opened this issue Mar 5, 2016 · 0 comments
Closed

Pysam #13

dalessandra opened this issue Mar 5, 2016 · 0 comments

Comments

@dalessandra
Copy link

Hi!

I had an issue with pysam.

I had this error message:
File "/home/apps/HiC-Pro/HiC-Pro_2.7.4b/scripts/mergeSAM.py", line 220, in
outfile = pysam.AlignmentFile(output, "wb", template=hr1)
AttributeError: 'module' object has no attribute 'AlignmentFile'
make: *** [bowtie_pairing] Error 1

My pysam version was 0.7.5
$ python
Python 2.7.2 (default, Feb 3 2012, 08:01:33)
[GCC 4.1.2 20080704 (Red Hat 4.1.2-51)] on linux2
Type "help", "copyright", "credits" or "license" for more information.

import pysam
print pysam.version
0.7.5

Pysam 0.7.5 does not have AlignmentFile.

Now I use Pysam 0.9 and it works great!

Thank you Nicolas and Dave for your help!!! :)

@NelleV NelleV closed this as completed Sep 7, 2016
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants