Pysam is a python module for reading and manipulating Samfiles. It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.
Questions tagged [pysam]
50 questions
0
votes
1 answer
Samtools pysam mate
I am using pysam to dome data mining on .bam files. I want to check if a read has a mapped mate. The command
mate = samfile.mate(read1)
throws an error if the mate is not mapped, so if I do
if samfile.mate(read1): ...
that throws an error, too.…
user2725109
- 2,286
- 4
- 27
- 46
0
votes
1 answer
Update Software Version in Anaconda
I have installed python and many other useful tools on my Ubuntu 14.04 using Anaconda. I installed pysam (htslib interface for python) using
conda install pysam
However this installs the old version (0.6). The current version is 0.8.4. How can I…
user2725109
- 2,286
- 4
- 27
- 46
0
votes
0 answers
how to convert a .BAI file into .TSV file using python script?
We have a file with "BAI" format and need to convert it to "TSV" format using python script.
We need a python script that converts .BAI file into "TSV".
I am a beginner at python scripting.
0
votes
1 answer
ValueError: error during iteration "Pysam"
I have ran into this error and I am having trouble resolving it. Here is it what I get:
Traceback (most recent call last):
File "afile.py", line 100, in
for col in bam.pileup( chrm, ps1, ps1+1,truncate=True):
File…
BioInformatician
- 97
- 2
- 12
-2
votes
1 answer
Command errored out with exit status 1: Python setup.py [...] When trying to install Pysam
I have been troubleshooting this issue for several days now and have had to draw the conclusion that i need help from you guys!
Info:
Python version: 3.8.2
Pip version: 20.0.2
Updated
Setuptools
Setuptools wheel
Python-language-server
Installing…
NIVE
- 1
- 2