Requirements:
- python >= 3.10
- BLAST: https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
Download the project:
git clone git@github.com: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
python -m flams.main [-h] (--in INPUT | --id id) [--range RANGE] [-o output] [-m MODIFICATION [MODIFICATION ...]] [-t NUM_THREADS] pos
Required arguments:
MODIFICATIONis one of: acetylation, lactylation, formylation, succinylation, hmgylation- one of:
INPUTis a path to fasta file with the queried protein (has to contain only 1 protein)idis a uniprot ID of the queried protein
posis 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 afterposto also search for modificationsNUM_THREADS(default: 1) is a BLAST parameteroutput(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 308 -m acetylation succinylation
python -m flams.main --id P57703 19 -m lactylation
Before commiting the code run:
black .
flake8 flams
To run all tests:
python -m unittest discover
To run a specific module:
python -m unittest test.test_display
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).
Manual: http://biopython.org/DIST/docs/tutorial/Tutorial.html#sec125
makeblastdb -in data/acetylation.faa -dbtype prot
Go to read_plm.py, change PLM_DATABASE to path of database, and OUTPUT to output path. Then run:
python read_plm.py
