Skip to content

cBioFormatter v0.2.0

Choose a tag to compare

View all tags
@tefirman tefirman released this 09 Jun 18:45
· 7 commits to main since this release
v0.2.0
a79b4f1

This release adds mutation data processing to cbioformatter, converting per-sample VCFs into cBioPortal-compatible mutation files alongside the existing clinical-data support.

Installation

pip install --upgrade cbioformatter

or with uv:

uv add cbioformatter

Requires Python 3.10 or newer.

Highlights

Mutation data processing

When sample_data contains a VCF_PATH column, ClinicalStudy now converts each VCF to MAF via a user-installed mafsmith, concatenates the per-sample MAFs into data_mutations.txt, and writes the matching meta_mutations.txt and case_lists/cases_sequenced.txt.

  • New constructor kwargs: ref_fasta_path (optional override; mafsmith uses its bundled reference by default) and mafsmith_path, with CBIOFORMATTER_REF_FASTA and CBIOFORMATTER_MAFSMITH_PATH env-var fallbacks.
  • Samples with null VCF_PATH values are skipped but still appear in cases_all.txt.
  • New error classes: MutationToolNotAvailableError, MutationConversionError, MissingReferenceFastaError.

Note: mafsmith does not currently populate the optional SWISSPROT column, so cBioPortal's Pfam-domain mutations view will be unavailable until nf-osi/mafsmith closes that gap.

Quick start

import pandas as pd
from cbioformatter import ClinicalStudy

# sample_data includes a VCF_PATH column pointing to each sample's VCF
study = ClinicalStudy(
    study_id="my_study",
    name="My Study",
    description="A short description",
    cancer_type="brca",
    sample_data=sample_df,
    patient_data=patient_df,
)

study.write_files(output_dir="./studies")

See the README for a fuller walkthrough.

What's next

  • cBioPortal study upload to a running local instance (#42).
  • See the open issues for the full backlog.

Full changelog

See CHANGELOG.md or the v0.1.0...v0.2.0 comparison for the complete list of changes.

Feedback

Please file an issue if you hit problems or have feature requests.

Assets 2
Loading