Hello all. I have been having issues on running a python script. I have tried to resolve it by uninstalling and reinstalling pysam since the error is about pysam mostly. below is the command and error i get.
$ python2.7 overlapping_reads.py Traceback (most recent call last): File "overlapping_reads.py", line 4, in <module> import pysam ImportError: No module named pysam
Can someone help?also, belo is portion of my script if that helps. Thanks
import argparse from collections import defaultdict import pysam def Parser(): the_parser = argparse.ArgumentParser() the_parser.add_argument( '--input', action="store", type=str, help="bam alignment file") the_parser.add_argument( '--minquery', type=int, help="Minimum readsize of query reads (nt) - must be an integer") the_parser.add_argument( '--maxquery', type=int, help="Maximum readsize of query reads (nt) - must be an integer") the_parser.add_argument( '--mintarget', type=int,
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This is most likely the case where you are using a
pipcommand associated with a different
Please share the exact command used to install
pysam. That could help decide what to do next to figure out where
pysammight be getting installed.
this is what I used. conda install -c bioconda pysam=0.9.1