OAS-wrapper 1.0

Python package to parse Observed antibody sequence data for easy reporting, visualization, annotation and alignment.

OAS_wrapper

A wrapper to parse Observed Antibody Space (OAS) data for better visualization, annotation and comparison of sequence to germline.

Functionalities

The scripts include functionalities to:

1. Provide basic metrics and visualizations of sequences and their annotations
2. Provide original IMGT sequences for V, D and J calls made in OAS data using IMGT reference database
3. Align sequence and germline to highlight regions of mismatches, providing positional information e.g.,

Example Output:  
Sequence: ATGCCGT  
Germline: ATGTCGT  
Aligned and Highlighted Differences:  
ATGC[RED]C[/RED]GT  
ATG[RED]T[/RED]CGT  
Indices of Differences: [3]  
Mapped Regions: [(3, 'CDR2')]  
--------------------------------------------------

5. Group data by germline, to infer sequences that originate from germline, including providing information on V, D and J annotations

Example Output:
germline,number_of_sequences,sequence,v_call,d_call,j_call,quality,source
IGHV1-69,3,ATGC,IGHV1,IGHD2,IGHJ4,High,Lab1
IGHV1-69,3,GCTA,IGHV1,IGHD2,IGHJ4,Medium,Lab2
IGHV1-69,3,ATGC,IGHV1,IGHD2,IGHJ4,High,Lab1
IGHV3-23,2,TAGC,IGHV3,IGHD3,IGHJ5,Low,Lab3
IGHV3-23,2,GCAT,IGHV3,IGHD3,IGHJ5,Medium,Lab2

7. Annotate sequence with CDRs and FWRs for easy inference of regions of interest

Example Output:  
Original Sequence: ATGCCGTAACTG  
Annotated Sequence: A(Unannotated)T(CDR1)GC(FWR1)GT(CDR2)AA(FWR2)CT(CDR3)G(Unannotated)  
--------------------------------------------------  
Row 2:  
Original Sequence: GATTACAGTGCTA  
Annotated Sequence: GAT(CDR1)TAC(FWR1)AG(CDR2)TG(FWR2)CTA(CDR3)  
--------------------------------------------------  

Project Organization

├── LICENSE            <- Open-source license if one is chosen
├── README.md          <- The top-level README for developers using this project.
├── data 
├── notebooks          <- Jupyter notebooks. Naming convention is a number (for ordering),
└── src                <- Source code for use in this project.

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