annkamsk / flams

A command line tool for identifying conserved lysine modification sites

Find Lysine Acetylation Modification Sites (working name)

Requirements:

• python >= 3.10
• BLAST: https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/

Usage

Setup

Download the project:

git clone [e-mail]:annkamsk/flams.git

cd flams

Create virtual environment and activate it:

python -m venv venv/

source venv/bin/activate

Install dependencies:

pip install -r requirements.txt

Run

python -m flams.main [-h] (--in INPUT | --id id) [--range RANGE] [-o output] [-m MODIFICATION [MODIFICATION ...]] [-t NUM_THREADS] pos

Required arguments:

• MODIFICATION is one of: acetylation, lactylation, formylation, succinylation, hmgylation
• one of:
  • INPUT is a path to fasta file with the queried protein (has to contain only 1 protein)
  • id is a uniprot ID of the queried protein
• pos is a position of lysine in the queried protein sequence where you look for modifications

Optional arguments:

• RANGE (default: 0) is an number of positions before and after pos to also search for modifications
• NUM_THREADS (default: 1) is a BLAST parameter
• output (default: out.tsv) is path to a csv file where the result will be saved

Example:

python -m flams.main --in P57703.fa --range 5 -o results.tsv -m acetylation succinylation 308

python -m flams.main --id P57703 -m lactylation 19

Development

Linters

Before commiting the code run: black . flake8 flams

Tests

To run all tests: python -m unittest discover

To run a specific module: python -m unittest test.test_display

Push a commit

First, create a new branch: git checkout -b <new-branch> should be a short (1-3 words) hyphen-separated name vaguely related to what you've been working on (eg. input-read etc). Don't stress too much about it. You'll be moved automatically to that branch.

git add .
git commit -m "{Short description of change}"
git push

To merge the code from the branch to the main branch, you need to create a pull request (can be done through the web interface).

Creating local BLAST database

Manual: http://biopython.org/DIST/docs/tutorial/Tutorial.html#sec125

makeblastdb -in data/acetylation.faa -dbtype prot

Parsing PLM database format

Go to read_plm.py, change PLM_DATABASE to path of database, and OUTPUT to output path. Then run: python read_plm.py