rosaak/ny-immuno-sanger

Jupyter Notebook

clone this repo

git clone https://github.com/rosaak/ny-immuno-sanger.git
cd ny-immuno-sanger

setting up the env

python3 -m venv env
source env/bin/activate
pip3 install -r requirements.txt

file structure

create a dir from_ny in the root of the project dir and put the ab1 files
Excel File

14 clones H3.xlsx

AB1 files

Sequencing results
├── VH
│   ├── FST470-hIgG1-011-A10_A10-VH60.ab1
│   ├── FST470-hIgG1-011-A11_A11-VH60.ab1
│   ├── FST470-hIgG1-011-A12_A12-VH60.ab1
│   ├── FST470-hIgG1-011-A1_A01-VH60.ab1
...
└── VL
    ├── FST470-hIgG1-011-A10_A10-VL79.ab1
    ├── FST470-hIgG1-011-A11_A11-VL79.ab1
    ├── FST470-hIgG1-011-A12_A12-VL79.ab1
...

Template

Templates
├── VH
│   ├── VH-FST470-hF-010-A01.gb
│   ├── VH-FST470-hF-010-A02.gb
│   ├── VH-FST470-hF-010-A05.gb
...
└── VL
    ├── VL-FST470-hF-010-A01.gb
    ├── VL-FST470-hF-010-A02.gb
    ├── VL-FST470-hF-010-A05.gb

what is happening

pick the pattern_sequence from the Excel file and search it against files in Sequencing results/{VH,VL}/*.ab1.
if there is a match then create a new dir Match_Res/{pattern_name} and put the matched .ab1 in it into VH and VL