xi-mzidentml-converter

xi-mzidentml-converter uses pyteomics (https://pyteomics.readthedocs.io/en/latest/index.html) to parse mzIdentML files (v1.2.0) and extract crosslink information. Results are written to a relational database (PostgreSQL or SQLite) using sqlalchemy.

Requirements:

python3.10

pipenv

sqlite3 or postgresql (these instruction use posrgresql)

1. Installation

Clone git repository :

git clone https://github.com/Rappsilber-Laboratory/xi-mzidentml-converter.git

cd into the repository:

cd xi-mzidentml-converter

Checkout python3 branch:

git checkout python3

2. create a postgresql role and database to use

sudo su postgres
psql
create database xiview;
create user xiadmin with login password 'your_password_here';
grant all privileges on database xiview to xiadmin;

find the hba.conf file in the postgresql installation directory and add a line to allow the xiadmin role to access the database: e.g.

sudo nano /etc/postgresql/13/main/pg_hba.conf

then add the line: local xiview xiadmin md5

then restart postgresql:

sudo service postgresql restart

3. Configure the python environment for the file parser

edit the file xiSPEC_ms_parser/credentials.py to point to your postgressql database. e.g. so its content is:

hostname = 'localhost'
username = 'xiadmin'
password = 'your_password_here'
database = 'xiview'
port = 5432

Set up the python environment:

cd xiSPEC_ms_parser
pipenv install --python 3.10

run create_db_schema.py to create the database tables:

python create_db_schema.py

parse a test dataset:

python process_dataset.py -d ~/PXD038060 -i PXD038060

The argument -d is the directory to read files from and -i is the project identifier to use in the database.

To run tests

Make sure we have the right db user available

psql -p 5432 -c "create role ximzid_unittests with password 'ximzid_unittests';"
psql -p 5432 -c 'alter role ximzid_unittests with login;'
psql -p 5432 -c 'alter role ximzid_unittests with createdb;'
psql -p 5432 -c 'GRANT pg_signal_backend TO ximzid_unittests;'

run the tests

pipenv run pytest