iseqcbioportal 0.0.6

Package for creating database from cBioPortal and annotating VCF with information from this database

ISEQcBioPortal

Scripts that allow you to:

1. Create/Update database from cBioPortal
2. Annotate VCF with information such as:

• number of samples with one or more mutations
• percentage of samples with one or more mutations

Install iseqcbioportal library

Optional steps (create virtual environment):

python3 -m venv venv
source venv/bin/activate

Obligatory steps:

python3 -m pip install --upgrade pip
pip3 install iseqcbioportal

Requirements

• python >=3.6
• pandas >= 1.4.2
• requests >= 2.28.1
• SQLAlchemy >= 1.4.0
• loguru >= 0.6.0
• pysam >= 0.21.0

Create databases

create_cbioportal_database

Annotate VCF

vcf_annotate_cbioportal --input-vcf "/path/to/input.vcf.gz" \
                        --studies "studyId" \
                        --output-vcf "/path/to/output.vcf.gz"