Hi, I am trying to run bam2stats from cgat-apps within a fresh conda environment containing just cgat-apps and its dependencies. My command is: cgat bam2stats --force-output --output-filename-patte...
I try to use pysam together with multiprocessing but got this error pysam.libcalignmentfile.AlignmentFile.__reduce_cython__ TypeError: no default __reduce__ ...
Jul 31, 2015 · Hi all, I am intending to work with SAM files in python, for which I need pysam. However, having installed pysam, I get the following error: >>> import pysam >>> samfile = pysam.AlignmentFile("ex1.bam", "rb") Traceback (most recent call last): File "", line 1, in AttributeError: 'module' object has no attribute 'AlignmentFile'
Hello, I have tried to install RNAindel using pip, and was able to successfully install: "Successfully installed rnaindel-3.0.2" However, when I try "rnaindel -h", I get the error: Traceback (most recent call last): File "/home/ch196471/...
Hi, I installed cgat-apps in a fresh Conda environment as follows: conda create -n cgat-apps conda activate cgat-apps conda install -c conda-forge -c bioconda cgat-apps I did not use mamba as this ...
AttributeError: module 'pysam.libcalignmentfile' has no attribute 'PileupColumn' PileupColumn was moved from libcalignmentfile to libcalignedsegment some years ago, and since pysam-developers/pysam#1007 (first released in 0.17.0) it no longer appears in libcalignmentfile.pxd at all — hence this error.
Show activity on this post. Am trying to use clr.AddReference and clr.AddReferenceToFile to import an assembly, but python (2.7) keeps making this error: Traceback (most recent call last): File "<pyshell#5>", line 1, in <module> clr.AddReference ("UnityEngine") AttributeError: 'module' object has no attribute 'AddReference'.
Pysam is a python module that makes it easy to read and manipulate mapped short read ... AttributeError – if htsfile is SAM formatted and thus has no index.
31.07.2015 · Hi all, I am intending to work with SAM files in python, for which I need pysam. However, having installed pysam, I get the following error: >>> import pysam >>> samfile = pysam.AlignmentFile("ex1.bam", "rb") Traceback (most recent call last): File "", line 1, in AttributeError: 'module' object has no attribute 'AlignmentFile'
Ok, Uninstalled using conda, also uninstalled using pip, then pip reinstalled seemed to fix it. Still getting some errors with other parts of the module but ...
AttributeError: module 'pysam.libcalignmentfile' has no attribute 'PileupColumn' #1055. Closed lucygarner opened this issue Oct 25, 2021 · 1 comment Closed ... module 'pysam.libcalignmentfile' has no attribute 'PileupColumn' ...
Hello, I have tried to install RNAindel using pip, and was able to successfully install: "Successfully installed rnaindel-3.0.2" However, when I try "rnaindel -h", I get the error: Traceback (most recent call last): File "/home/ch196471/...
Attempting a pip install (after updating pip and wheel with "python -m pip install ... AttributeError: module 'pysam.libcalignmentfile' has no attribute ...