zavolanlab / tin-score-calculation

Given a set of BAM files and a gene annotation BED file, calculates the Transcript Integrity Number (TIN) for each transcript.

Geek Repo:Geek Repo

Github PK Tool:Github PK Tool

Eliminate dependencies

fgypas opened this issue · comments

Is your feature request related to a problem? Please describe.
I was looking at the dependencies of it seems that we could eliminate some of them. More specifically do we really need the guppy package?

from guppy import hpy

Describe the solution you'd like
The maintenance of the package will be easier if we will not use the specific package.

@mzavolan @meric466 @AngryMaciek Do you think it can be eliminated?

We should remove this; I went through the script and conclude that it is not used anymore in the code:

Great. This means that we don't have to care for guppy in the future. I spent a lot of time making guppy3 available in conda-forge: conda-forge/staged-recipes#14913 and I am afraid that it will cause issues in the future.

Can someone from you work on it?

Note that this might also fix #18

Also, forgot to mention. We don't have to do that for this release, but it would be good to fix it before we publish zarp.