https://github.com/hammerlab/immuno
Use somatic mutations to choose a personalized cancer vaccine (tumor-specific immunogenic peptides)
https://github.com/hammerlab/immuno
Last synced: about 1 year ago
JSON representation
Use somatic mutations to choose a personalized cancer vaccine (tumor-specific immunogenic peptides)
- Host: GitHub
- URL: https://github.com/hammerlab/immuno
- Owner: hammerlab
- License: apache-2.0
- Created: 2014-03-06T19:56:01.000Z (about 12 years ago)
- Default Branch: master
- Last Pushed: 2016-09-23T20:53:08.000Z (over 9 years ago)
- Last Synced: 2025-04-04T09:44:41.949Z (about 1 year ago)
- Language: Python
- Size: 2.46 MB
- Stars: 15
- Watchers: 12
- Forks: 3
- Open Issues: 36
-
Metadata Files:
- Readme: README.md
- License: LICENSE.txt
Awesome Lists containing this project
README
# RETIRED: See [vaxrank](https://github.com/hammerlab/vaxrank) and [epidisco](https://github.com/hammerlab/epidisco) instead
## Immunotherapy Pipeline
### Status
[](https://travis-ci.org/hammerlab/immuno)
### Usage
#### From peptide string
```sh
python mutation_report.py --string EDLTVKIGDFGLATEKSRWSGSHQFEQLS --hla "HLA-B*35:01"
```
#### From input file
```sh
python mutation_report.py --input-file <.vcf, .maf, .tab, .fasta> --hla-file
```
If VCF file is input, it will be annotated w/ gene information and Ensembl transcripts, otherwise input an annotated SnpEFF VCF file.
If you don't either an `hla` or `hla-file` then the default "HLA:A*02:01" will be used.
### Options:
* `--input-file`: Input file containing somatic variants (one of MAF, VCF, or SnpEff annotated VCF)
* `--string`: String of amino acids, with optional annotation of a mutated region between underscores (i.e. QYS\_LL\_Q)
* `--hla`: Comma separated list of HLA alleles.
* `--hla-file`: Text file containing one HLA allele per line.
* `--peptide-length`: Length of vaccine peptide (window around mutation, default 31)
* `--min-peptide-padding`: Minimum number of wildtype residues before or after a mutation
* `--print-epitopes`: Print dataframe with epitope scores
* `--print-peptides`: Print dataframe with vaccine peptide scores
* `--output-epitopes-file`: CSV output file for dataframe containing scored epitopes
* `--output-report-file`: Path to HTML report containing scored vaccine peptides and epitopes
* `--random-mhc`: Random values instead for MHC binding prediction
* `--iedb-mhc`: Use IEDB's web API for MHC binding
* `--skip-mhc`: Don't predict MHC binding
* `--quiet`: Suppress verbose output
### Requirements
* [datacache](https://github.com/hammerlab/datacache)
* [epitopes](https://github.com/hammerlab/epitopes)
* [nose](https://nose.readthedocs.org/en/latest/)
* [NumPy](http://www.numpy.org/)
* [pandas](http://pandas.pydata.org/)
* [BioPython](http://biopython.org/wiki/Main_Page)
You must either have [netMHCpan](http://www.cbs.dtu.dk/services/NetMHCpan/) installed locally or pass the `iedb-mhc` flag to use a web-based MHC binding predictor.