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bio-arc-0.1.1
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Antigen Receptor Classifier
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | bio-arc-0.1.1 |
| نام | bio-arc |
| نسخه کتابخانه | 0.1.1 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Austin Crinklaw |
| ایمیل نویسنده | acrinklaw@lji.org |
| آدرس صفحه اصلی | https://github.com/iedb/arc |
| آدرس اینترنتی | https://pypi.org/project/bio-arc/ |
| مجوز | - |
# ARC (Antigen Receptor Classifier)
### Authors: Austin Crinklaw, Swapnil Mahajan
## Requirements:
- Linux OS
- [HMMER3](http://hmmer.org/)
- NCBI Blast+
- Python 3+
- Python packages: Pandas, BioPython
## Installation:
We provide a Dockerfile for ease of use.
ARC can also be downloaded through PyPI using the following pip command.
```shell
pip install bio-arc
```
### Testing Installation:
A quick check for proper dependencies and successful installation can be performed by navigating to your pip package install directory (which can be located by executing ```pip show bio-arc```) and running the following command:
```shell
python3 -m arc_test
```
Passing all unit-tests means that your system is configured properly and ready to classify some protein sequences.
## Usage:
### Input
- A fasta format file with one or more protein sequences.
```
>1WBZ_A_alpha I H2-Kb
MVPCTLLLLLAAALAPTQTRAGPHSLRYFVTAVSRPGLGEPRYMEVGYVDDTEFVRFDSDAENPRYEPRARWMEQEGPEYWERETQKAKGNEQSFRVDLRTLLGYYNQSKGGSHTIQVISGCEVGSDGRLLRGYQQYAYDGCDYIALNEDLKTWTAADMAALITKHKWEQAGEAERLRAYLEGTCVEWLRRYLKNGNATLLRTDSPKAHVTHHSRPEDKVTLRCWALGFYPADITLTWQLNGEELIQDMELVETRPAGDGTFQKWASVVVPLGKEQYYTCHVYHQGLPEPLTLRWEPPPSTVSNMATVAVLVVLGAAIVTGAVVAFVMKMRRRNTGGKGGDYALAPGSQTSDLSLPDCKVMVHDPHSLA
>1WBZ_B_b2m I H2-Kb
MARSVTLVFLVLVSLTGLYAIQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDWSFYILAHTEFTPTETDTYACRVKHASMAEPKTVYWDRDM
```
### Commands
- Using Fasta file as an input:
```shell
python -m ARC classify -i /path/to/input.fasta -o /path/to/output.csv
```
### Output
- Output file has 4 columns in CSV format.
- First column named 'ID' is the description provoded in the fasta for each sequence.
- Second column named 'class' is the assigned molecule class for each sequence.
- e.g. MHC-I, MHC-II, BCR or TCR.
- The third column named 'chain_type' is the assigned chain type for each sequence.
- e.g. alpha, beta, heavy, lambda, kappa, scFv, TscFv or construct. These will also be labelled as V for variable domain or C for constant domain.
- The fourth column named 'calc_mhc_allele' is the MHC allele identified using groove domain similarity to MRO alleles.
| ID | class | chain_type | calc_mhc_allele|
|---------------------------------------- |------- |----------- |---------------|
| 1WBY_A_alpha I H2-Db | MHC-I | alpha V | |
| 1WBY_B_b2m I H2-Db | | | |
| 1HQR_A_alpha II HLA-DRA*01:01/DRB5*01:01| MHC-II | alpha C | HLA-DRA*01:01 |
| 1HQR_B_beta II HLA-DRA*01:01/DRB5*01:01 | MHC-II | beta C | HLA-DRB5*01:01 |
| 2CMR_H_heavy | BCR | heavy V | |
| 2CMR_L_light | BCR | kappa C | |
| 4RFO_L_light | BCR | lambda V | |
| 3UZE_A_heavy | BCR | scFv | |
| 1FYT_D_alpha | TCR | alpha V | |
| 1FYT_E_beta | TCR | beta C | |
| 3TF7_C_alpha | TCR | TscFv | |
## How it works:
- BCR and TCR chains are identified using HMMs. A given protein sequence is searched against HMMs built using BCR and TCR chain sequences from IMGT. HMMER is used to align an input sequence to the HMMs.
- MHC class I (alpha1-alpha2 domains) and MHC class I alpha and beta chain HMMs are downloaded from Pfam website. An input protein sequence is searched against these HMMs. A HMMER bit score threshold of 25 was used to identify MHC chain sequences.
- To identify MHC alleles, groove domains (G-domains) are assigned based on the MRO repository.
- IgNAR sequences are identified through querying against a custom blast database.
## References:
Several methods for HMMER result parsing were sourced from ANARCI.
[Dunbar J and Deane CM. ANARCI: Antigen receptor numbering and receptor classification. Bioinformatics (2016)](https://academic.oup.com/bioinformatics/article/32/2/298/1743894)
نیازمندی
| مقدار | نام |
|---|---|
| - | biopython |
| - | numpy |
| - | pandas |
نحوه نصب
نصب پکیج whl bio-arc-0.1.1:
pip install bio-arc-0.1.1.whl
نصب پکیج tar.gz bio-arc-0.1.1:
pip install bio-arc-0.1.1.tar.gz