bio-ting 1.1.0
ting - T cell receptor interaction grouping
License: MIT License

[![PyPI version](https://img.shields.io/pypi/v/bio-ting?logo=PyPI)](https://pypi.org/project/bio-ting/)
[![Bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](https://bioconda.github.io/recipes/bio-ting/README.html)
# ting - T cell receptor interaction grouping

ting is a tool for clustering large scale T cell receptor repertoires by antigen-specificity

## Synopsis

ting [options] -t sample.tsv -r reference.tsv -k kmer.tsv -o output.tsv

## Options

Required Input
~~~~~~~~~~~~~~

The user must provide a list of CDR3b sequences.
For compatibility reasons the tab seperated table of TCR sequences required for gliph is supported, too.

    --tcr_sequences tcr_sequences   The format of the table is tab delimited, expecting only the first
                                    column. The header is optional, but if included only use column
                                    names as shown in the example.

    --kmer_file K-MER_FILE          The k-mer file holds all 2-, 3- and 4-mers considered for local
                                    clustering. If file does not exist it will automatically be
                                    generated.

    --reference                     Reference file of naive CDR3 amino acid sequences in fasta-format.
                                    Used as control set by Fisher's exact test.

Example:

CDR3b		TRBV	TRBJ	CDR3a		TRAV		TRAJ	Sample-ID
CAADTSSGANVLTF	TRBV30	TRBJ2-6	CALSDEDTGRRALTF	TRAV19		TRAJ5	09/02171
CAATGGDRAYEQYF	TRBV2	TRBJ2-7	CAASSGANSKLTF	TRAV13-1	TRAJ56	03/04922
CAATQQGETQYF	TRBV2	TRBJ2-5	CAASYGGSARQLTF	TRAV13-1	TRAJ22	02/02591
CACVSNTEAFF	TRBV28	TRBJ1-1	CAGDLNGAGSYQLTF	TRAV25		TRAJ28	PBMC8631
CAGGKGNSPLHF	TRBV2	TRBJ1-6	CVVLRGGSQGNLIF	TRAV12-1	TRAJ42	02/02071
CAGQILAGSDTQYF	TRBV6-4	TRBJ2-3	CATASGNTPLVF	TRAV17		TRAJ29	09/00181
CAGRTGVSTDTQYF	TRBV5-1	TRBJ2-3	CAVTPGGGADGLTF	TRAV41		TRAJ45	02/02591
CAGYTGRANYGYTF	TRBV2	TRBJ1-2	CVVNGGFGNVLHC	TRAV12-1	TRAJ35	01/08733

Optional Input



    --use_structural_boundaries     If set, the first and last three amino acids will be included
                                    in kmer counting and global clustering.

    --no_global                     No global clustering will be performed.

    --no_local                      No local clustering will be performed.

    --min_kmer_occurence            Only kmers which occure at least min_kmer_occurences times in the
                                    sequence sample set will be taken in account. Default is 3.
    
    --max_p_value                   p-value threshold for identifying significant motifs by fisher exact test
    
    --gliph_minp                    probability threshold for identifying significant motifs by gliph test

    --stringent_filtering           Only TCRs starting with a cystein and ending with phenylalanine will be
                                    used (IGMT definition of CDR3 region). Default: False
                                    
    --kmers_gliph                   If set kmers are identified by the non-deterministic approach as implemented by gliph

~~~~~~~~~~~~~~

## Install

ting can be run from source or installed via [PyPI](https://pypi.org/project/bio-ting/) or [bioconda](https://bioconda.github.io/recipes/bio-ting/README.html?highlight=bio-ting#recipe-Recipe%20&#x27;bio-ting&#x27;)

#### PiPI:
    pip install bio-ting

#### conda:
    conda install -c bioconda bio-ting

## Example

Example repertoires can be obtained from `repertoires.tar.gz` included in the `example_data`-folder

References have been created by the authors of [gliph](https://github.com/immunoengineer/gliph) ([Glanville et al.](https://www.ncbi.nlm.nih.gov/pubmed/28636589)).

```
ting --tcr_sequences R205-L01-D704D504.tsv --reference reference.fasta --kmer_file R205-L01-D704D504_kmers.tsv -o R205-L01-D704D504_results.tsv
```

## Citation

For citation please refere to our preprint [Rapid T cell receptor interaction grouping with ting](https://www.biorxiv.org/content/10.1101/2020.05.04.069914v1).
A peer review is currently in process.