presplit.py error no attribute 'is_supplementary'

[hwick]

Hello,
I'm trying to run presplit.py on our data, but running into the following issue:

Traceback (most recent call last):
  File "/home/hwick/top2b/master/interaction/scripts/presplit_map.py", line 215, in <module>
    read3.is_supplementary=True
AttributeError: 'pysam.calignmentfile.AlignedSegment' object has no attribute 'is_supplementary'

I'm using the most recent version of the presplit_map.py with python 2.7.6, and bowtie 1.2.2. It failed on this error without producing any output after running for a week.
Any assistance you can provide would be greatly appreciated.

[LTLA]

I updated this a while ago to use Python 3, and I no longer know how it behaves on Python 2. By the looks of things, I guess it doesn't work on Python 2 anymore.

A week is a long time for this script to run. Most of the time is spent in alignment, and while bowtie2 is not particularly fast, you can usually give it some threads to get it moving along.

[hwick]

Thanks for the response. My understanding was that pysam does not work on python 3, but I may have misunderstood based on our own server's set up. I really appreciate your response, thank you