ISV package

Python package for easy prediction of pathogenicity Copy Number Variants (CNVs)

If you mention or use the ISV tool, please cite our article

https://www.nature.com/articles/s41598-021-04505-z

Install

Install with `pip install isv`

This will also automatically install all required additional packages. Thus it is recommended to install the package in a separate environment (e.g. uv, virtualenv, conda, ...)

Package url: https://pypi.org/project/isv/

Module reference available at https://tsladecek.github.io/isv_package/

Modules

The package contains a wrapper function:

`isv.isv(cnvs, proba, shap)`

which automatically annotates and predicts cnvs provided in a list, np.array or pandas DataFrame format represented in 4 columns: chromosome, start (grch38), end (grch38) and cnv_type

The proba parameter controls whether probabilities should be calculated
The shap parameter controls whether shap values should be calculated

and a Wrapper class (which is recommended):

`isv.ISV(cnvs)`

with methods:

ISV.predict(proba)
ISV.shap(data=None)
- where the data argument is optional
ISV.waterfall(cnv_index)
- for creating an interactive waterfall plot for a CNV at index cnv_index

The main subfunctions of the package are:

1. `isv.annotate(cnvs)`

annotates cnvs provided in a list, np.array or pandas DataFrame format represented in 4 columns: chromosome, start (grch38), end (grch38) and cnv_type
Returns an annotated dataframe which can be used as an input to following two functions

2. `isv.predict(annotated_cnvs, proba)`

returns an array of isv predictions. annotated_cnvs represents annotated cnvs returned by the annotate function

3. `isv.shap_values(annotated_cnvs)`

calculates shap values for given CNVs. annotated_cnvs represents annotated cnvs returned by the annotate function

For example

using the simple wrapper

from isv import isv


cnvs = [
    ["chr8", 100000, 500000, "DEL"],
    ["chrX", 52000000, 55000000, "DUP"]
] 

results = isv(cnvs, proba=True, shap=True)

using the ISV class

from isv import ISV


cnvs = [
    ["chr8", 100000, 500000, "DEL"],
    ["chrX", 52000000, 55000000, "DUP"]
] 

cnv_isv = ISV(cnvs)
predictions = cnv_isv.predict(proba=True)
shap_vals = cnv_isv.shap()
cnv_isv.waterfall(cnv_index=1)

Can be also used as a command line tool

isv -i <input_cnvs>.bed -o <outputpath> [-p] [-sv]

where the input should be a list of CNVs in a bed format, with columns: chromosome, start (grch38), end (grch38) and cnv_type

[!NOTE] The first row must contain column names

Results will be saved in a tab separated file at path specified by user

Optionally, use following flags:

-p: whether probabilities should be returned
-sv: whether shap values should be calculated

For example

isv -i examples/loss_gain_cnvs.bed -o examples/loss_gain_cnvs_out.bed -p -sv

Metadata

Release files for isv 0.3.17

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for isv 0.3.17
File	Size	Uploaded
isv-0.3.17.tar.gz	6.0 MB	Apr 9, 2026	Details

Built distribution (wheel)

Table of built distributions (wheels) for isv 0.3.17
File	Interpreter	ABI	Platform	Reset
isv-0.3.17-py3-none-any.whl 6.0 MB Apr 9, 2026	Python 3	none	any	Details

Total release size: 11.9 MB

Release files / isv-0.3.17.tar.gz

Download URL	isv-0.3.17.tar.gz
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Release files / isv-0.3.17-py3-none-any.whl

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Uploaded via	`uv/0.11.5 {"installer":{"name":"uv","version":"0.11.5","subcommand":["publish"]},"python":null,"implementation":{"name":null,"version":null},"distro":{"name":"Ubuntu","version":"24.04","id":"noble","libc":null},"system":{"name":null,"release":null},"cpu":null,"openssl_version":null,"setuptools_version":null,"rustc_version":null,"ci":true}`