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Create IGoR models and calculate the generation probability of V(D)J and CDR3 sequences.

Project description

ImmunoProbs

Build Status PyPI version shields.io PyPI pyversions PyPI license

Create IGoR models and calculate the generation probability of V(D)J and CDR3 sequences.

For installation, use cases and a tutorial, please have a look at the ImmunoProbs wiki page.

Development

Development of ImmunoProbs is in an active state. If you would like to see new features, please open a new issue.

It is also possible to help out ImmunoProbs development by forking this project and creating a pull request to submit new features.

When using a forked copy ImmunoProbs, make sure to have the correct Python version installed. Install the local Python development requirements using the make command:

make setup

Package structure

immuno_probs
├── __init__.py
├── alignment
│   ├── __init__.py
│   ├── align_read.py
│   └── muscle_aligner.py
├── cdr3
│   ├── __init__.py
│   ├── anchor_locator.py
│   └── olga_container.py
├── cli
│   ├── __init__.py
│   ├── __main__.py
│   ├── build_igor_model.py
│   ├── evaluate_seqs.py
│   ├── generate_seqs.py
│   └── locate_cdr3_anchors.py
├── data
│   ├── human_b_heavy
│   │   ├── J_gene_CDR3_anchors.csv
│   │   ├── V_gene_CDR3_anchors.csv
│   │   ├── genomic_D.fasta
│   │   ├── genomic_J.fasta
│   │   ├── genomic_V.fasta
│   │   ├── model_marginals.txt
│   │   └── model_params.txt
│   ├── human_t_alpha
│   │   ├── J_gene_CDR3_anchors.csv
│   │   ├── V_gene_CDR3_anchors.csv
│   │   ├── genomic_J.fasta
│   │   ├── genomic_V.fasta
│   │   ├── model_marginals.txt
│   │   └── model_params.txt
│   ├── human_t_beta
│   │   ├── J_gene_CDR3_anchors.csv
│   │   ├── V_gene_CDR3_anchors.csv
│   │   ├── genomic_D.fasta
│   │   ├── genomic_J.fasta
│   │   ├── genomic_V.fasta
│   │   ├── model_marginals.txt
│   │   └── model_params.txt
│   ├── mouse_t_beta
│   │   ├── J_gene_CDR3_anchors.csv
│   │   ├── V_gene_CDR3_anchors.csv
│   │   ├── genomic_D.fasta
│   │   ├── genomic_J.fasta
│   │   ├── genomic_V.fasta
│   │   ├── model_marginals.txt
│   │   └── model_params.txt
│   └── tutorial_model
│       ├── CDR3_sequences.csv
│       └── VDJ_sequences.csv
├── model
│   ├── __init__.py
│   ├── default_models.py
│   ├── igor_interface.py
│   └── igor_loader.py
└── util
    ├── __init__.py
    ├── cli.py
    ├── constant.py
    ├── conversion.py
    ├── exception.py
    ├── io.py
    └── processing.py

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