<commit_before>[![Build Status](https://travis-ci.org/hammerlab/vaxrank.svg?branch=master)](https://travis-ci.org/hammerlab/vaxrank) [![Coverage Status](https://coveralls.io/repos/github/hammerlab/vaxrank/badge.svg?branch=master)](https://coveralls.io/github/hammerlab/vaxrank?branch=master)

# vaxrank

Selection of mutated protein fragments for therapeutic personalized cancer vaccines.

## Usage

```sh

vaxrank \
    --vcf test/data/b16.f10/b16.vcf \
    --bam test/data/b16.f10/b16.combined.bam \
    --vaccine-peptide-length 25 \
    --mhc-predictor netmhc \
    --mhc-alleles H2-Kb,H2-Db \
    --padding-around-mutation 5 \
    --output-ascii-report vaccine-peptides.txt \
    --output-pdf-report vaccine-peptides.pdf \
    --output-html-report vaccine-peptides.html
```

## Installation

Vaxrank can be installed using [pip](https://packaging.python.org/installing/#use-pip-for-installing):

```
pip install vaxrank
```

Note: to generate PDF reports, you first need to install [wkhtmltopdf](http://wkhtmltopdf.org/), which you can do (on OS X) like so:

```
brew install Caskroom/cask/wkhtmltopdf
````<commit_msg>Update README with development instructions<commit_after>[![Build Status](https://travis-ci.org/hammerlab/vaxrank.svg?branch=master)](https://travis-ci.org/hammerlab/vaxrank) [![Coverage Status](https://coveralls.io/repos/github/hammerlab/vaxrank/badge.svg?branch=master)](https://coveralls.io/github/hammerlab/vaxrank?branch=master)

# vaxrank

Selection of mutated protein fragments for therapeutic personalized cancer vaccines.

## Usage

```sh

vaxrank \
    --vcf test/data/b16.f10/b16.vcf \
    --bam test/data/b16.f10/b16.combined.bam \
    --vaccine-peptide-length 25 \
    --mhc-predictor netmhc \
    --mhc-alleles H2-Kb,H2-Db \
    --padding-around-mutation 5 \
    --output-ascii-report vaccine-peptides.txt \
    --output-pdf-report vaccine-peptides.pdf \
    --output-html-report vaccine-peptides.html
```

## Installation

Vaxrank can be installed using [pip](https://packaging.python.org/installing/#use-pip-for-installing):

```
pip install vaxrank
```

Note: to generate PDF reports, you first need to install [wkhtmltopdf](http://wkhtmltopdf.org/), which you can do (on OS X) like so:

```
brew install Caskroom/cask/wkhtmltopdf
````

# Development

To install Vaxrank for local development, you may do the below:

```
git clone git@github.com:hammerlab/vaxrank.git
conda create -q -n vaxrank-dev-env python=3.5.2 numpy scipy nose pandas pylint
source activate vaxrank-dev-env
pip install -r requirements.txt
pip install .
pyensembl install --release 85 --species human
pyensembl install --release 85 --species mouse
```

You should run the linter and the test suite as you work on Vaxrank (and these will be run automatically by our continuous integration server up on a PR being made).

```
./lint.sh
nosetests test
```
{'fraction_non_alphanumeric': 0.13906359189378056, 'fraction_numerical': 0.0143256464011181, 'mean_word_length': 3.860780984719864, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 10, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 1, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 1, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '3886231', 'n_tokens_mistral': 1059, 'n_tokens_neox': 961, 'n_words': 223}