Pysam

[dalessandra]

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!!! :)