the difference between pysam and pybam

Question

[Nobody]

hi everyone ! I am a beginner in bioinformatics, iwonder what the difference between pysam and bybam and what they do as role.

they are coded by python 2 ?

thank you in advanced

Answer 1

[ATpoint]

Quoting the Pysam Github repo description:

Pysam is a Python module for reading and manipulating SAM/BAM/VCF/BCF files. It's a lightweight wrapper of the htslib C-API, the same one that powers samtools, bcftools, and tabix.

I do not know which pybam you are referring to, you'd need to provide a link. It is probably any other project aiming to write software for NGS data manipulation in python.

[Ram]

OP is probably referring to this: https://github.com/JohnLonginotto/pybam

Author of that software claims it is probably faster than pysam, which is a bold claim to make, given their tool doesn't seem to use C++ or htslib.

EDIT: That software is abandonware made by someone with a bit of a holier-than-thou stance: https://github.com/JohnLonginotto/pybam/issues/7#issuecomment-427638328