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.
python3.10
pipenv
sqlite3 or postgresql (these instruction use posrgresql)
Clone git repository :
git clone https://github.com/Rappsilber-Laboratory/xi-mzidentml-converter.git
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
edit the file xi-mzidentml-converter/config/database.ini to point to your postgressql database. e.g. so its content is:
[postgresql]
host=localhost
database=xitest
user=xiadmin
password=your_password_here
port=5432
Set up the python environment:
cd x-mzidentml-converter
pipenv install --python 3.10
run create_db_schema.py to create the database tables:
python database/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.
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