cellme
Convert a human cell line identifier into a truth-track VCF of its known mutations.
Introduction
cellme builds a truth/known VCF for a cell line by resolving a name such as MOLT-4 to a Cancer Cell Line Encyclopedia sample, fetching that sample's somatic mutations from the cBioPortal REST API, and writing them as a sorted VCF.
The mutation source is the ccle_broad_2019 study.
CCLE reports its coordinates against hg19 (GRCh37); by default cellme lifts them to hg38 (GRCh38), and --build hg19 keeps the native coordinates.
Installation
Install the release from PyPI with pip:
pip install cellme
Usage
Write an hg38 truth track for the cell line MOLT-4 to a file:
cellme "MOLT-4" --build hg38 --reference /ref/hg38.fa --output MOLT-4.hg38.vcf.gz
[!IMPORTANT] Always pass
--referencewith a FASTA for the build you target, as shown above. It ensures the correct anchor bases are set for insertions and deletions. Without it, indel anchor bases fall back to a placeholderNand those records are markedANCHOR=placeholder.
The build keys are hg38 and hg19 (the Ensembl names GRCh38 and GRCh37 are accepted as aliases).
The query is matched case-insensitively on the leading cell line token, so MOLT-4, MOLT4, and the full MOLT4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE sample ID all resolve to the same sample.
VCF INFO Fields
Every record is annotated with compact, self-describing INFO fields.
| Key | Type | Description |
|---|---|---|
GENE |
String | HUGO gene symbol. |
PROTEIN_CHANGE |
String | Protein-level change in CCLE short form (HGVS p.-like), e.g. R306*. |
VARIANT_CLASS |
String | Variant classification (MAF-style), e.g. Missense_Mutation. |
VARIANT_TYPE |
String | Sequence alteration type reported by CCLE: SNP, DNP, INS, or DEL. |
CELL_LINE |
String | Cell line resolved from the query. |
SAMPLE_ID |
String | CCLE sample identifier for the cell line. |
ENTREZ |
Integer | NCBI Entrez gene identifier. |
REFSEQ |
String | RefSeq mRNA accession for the annotated transcript. |
PROTEIN_POS |
String | Affected protein position or range, 1-based. |
SOURCE |
String | Source database and study, e.g. cBioPortal CCLE ccle_broad_2019. |
ORIGINAL_BUILD |
String | Genome build of the source coordinates before any liftover. |
ORIGINAL_LOCUS |
String | Original locus before liftover in UCSC position format, e.g. chr17:7577022. |
LIFTED |
Flag | Coordinate was lifted from ORIGINAL_BUILD to the output reference build. |
ANCHOR |
String | Provenance of the indel anchor base: reference or placeholder. |
The ID column is set to a stable gene:proteinChange token where one is available, for example TP53:R306*, and falls back to gene:chrom:pos otherwise.
Development and Testing
See the contributing guide for more information.
1 maintainer
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
Filter files by name, interpreter, ABI, and platform.
If you're not sure about the file name format, learn more about wheel file names.
Copy a direct link to the current filters
File details
Details for the file cellme-1.3.0.tar.gz.
File metadata
- Download URL: cellme-1.3.0.tar.gz
- Upload date:
- Size: 96.7 kB
- Tags: Source
- Uploaded using Trusted Publishing? Yes
- Uploaded via:
twine/7.0.0 CPython/3.13.14
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 |
e2a997d723ef94d19889d828f42bf632079e5417d97bdefdaec616e5b6b5f809
|
|
| MD5 |
1aac0d5669a69b02ea280b2e6b47666f
|
|
| BLAKE2b-256 |
c578942358cd0c8c59bf0fd0ec82214e73c3d915753308ddccda7a4d03745efb
|
Provenance
The following attestation bundles were made for cellme-1.3.0.tar.gz:
Publisher:
publish_cellme.yml on clintval/cellme
-
Statement:
-
Statement type:
https://in-toto.io/Statement/v1 -
Predicate type:
https://docs.pypi.org/attestations/publish/v1 -
Subject name:
cellme-1.3.0.tar.gz -
Subject digest:
e2a997d723ef94d19889d828f42bf632079e5417d97bdefdaec616e5b6b5f809 - Sigstore transparency entry: 2733255029
- Sigstore integration time:
-
Permalink:
clintval/cellme@21a8a0143ac5ece258d98546d45f1e1a33f9283a -
Branch / Tag:
refs/tags/1.3.0 - Owner: https://github.com/clintval
-
Access:
public
-
Token Issuer:
https://token.actions.githubusercontent.com -
Runner Environment:
github-hosted -
Publication workflow:
publish_cellme.yml@21a8a0143ac5ece258d98546d45f1e1a33f9283a -
Trigger Event:
push
-
Statement type:
File details
Details for the file cellme-1.3.0-py3-none-any.whl.
File metadata
- Download URL: cellme-1.3.0-py3-none-any.whl
- Upload date:
- Size: 19.2 kB
- Tags: Python 3
- Uploaded using Trusted Publishing? Yes
- Uploaded via:
twine/7.0.0 CPython/3.13.14
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 |
23e9e892e9cbc3b601efe8fd7c2a7c305d012f0930b976d9489787efd79a1111
|
|
| MD5 |
82830fe5cc7dcb1944eed5daafa89f62
|
|
| BLAKE2b-256 |
2c28d8fbcbec39337bd01c61e63a050ac840e75e1326165b6ccddace8f1e967d
|
Provenance
The following attestation bundles were made for cellme-1.3.0-py3-none-any.whl:
Publisher:
publish_cellme.yml on clintval/cellme
-
Statement:
-
Statement type:
https://in-toto.io/Statement/v1 -
Predicate type:
https://docs.pypi.org/attestations/publish/v1 -
Subject name:
cellme-1.3.0-py3-none-any.whl -
Subject digest:
23e9e892e9cbc3b601efe8fd7c2a7c305d012f0930b976d9489787efd79a1111 - Sigstore transparency entry: 2733255055
- Sigstore integration time:
-
Permalink:
clintval/cellme@21a8a0143ac5ece258d98546d45f1e1a33f9283a -
Branch / Tag:
refs/tags/1.3.0 - Owner: https://github.com/clintval
-
Access:
public
-
Token Issuer:
https://token.actions.githubusercontent.com -
Runner Environment:
github-hosted -
Publication workflow:
publish_cellme.yml@21a8a0143ac5ece258d98546d45f1e1a33f9283a -
Trigger Event:
push
-
Statement type:
