ISEQcBioPortal
Scripts that allow you to:
- Create/Update database from cBioPortal
- 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"
1 maintainer
Metadata
1 maintainer
Release files for iseqcbioportal 0.0.6
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Source distribution (sdist)
| File | Size | Uploaded | Provenance | |
|---|---|---|---|---|
| iseqcbioportal-0.0.6.tar.gz | 6.7 kB | Without provenance | Details |
Release files / iseqcbioportal-0.0.6.tar.gz
| Download URL | iseqcbioportal-0.0.6.tar.gz |
|---|---|
| Size | 6.7 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
317e783bd604c5f3f594a1adee19d81fabf99b7858902303e9cad75094417b2b
|
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/4.0.1 CPython/3.8.10
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Security for iseqcbioportal 0.0.6
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