ISV package

Python pip 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. 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

1. using the simple wrapper

from isv import isv


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

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

2. 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. Make sure to:

1. clone the repository (https://github.com/tsladecek/isv_package)

2. install requirements, e.g.

virtualenv venv
source venv/bin/activate
pip install -r requirements.txt

3. Use ISV!

python isv_cmd.py -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

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

python isv_cmd.py -i examples/loss_gain_cnvs.bed -o examples/loss_gain_cnvs_out.bed -p -sv