# xi-mzidentml-converter
[](https://opensource.org/licenses/Apache-2.0)
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```
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"description": "# xi-mzidentml-converter\n\n[](https://opensource.org/licenses/Apache-2.0)\n\nxi-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.\n\n### Requirements:\npython3.10\n\npipenv\n\nsqlite3 or postgresql (these instruction use posrgresql)\n\n## 1. Installation\n\nClone git repository :\n\n```git clone https://github.com/Rappsilber-Laboratory/xi-mzidentml-converter.git```\n\ncd into the repository:\n\n```cd xi-mzidentml-converter```\n\nCheckout python3 branch:\n\n```git checkout python3```\n\n## 2. create a postgresql role and database to use\n\n```\nsudo su postgres\npsql\ncreate database xiview;\ncreate user xiadmin with login password 'your_password_here';\ngrant all privileges on database xiview to xiadmin;\n```\n\nfind the hba.conf file in the postgresql installation directory and add a line to allow the xiadmin role to access the database:\ne.g.\n```\nsudo nano /etc/postgresql/13/main/pg_hba.conf\n```\nthen add the line:\n`local xiview xiadmin md5`\n\nthen restart postgresql:\n```\nsudo service postgresql restart\n```\n\n## 3. Configure the python environment for the file parser\n\nedit the file xiSPEC_ms_parser/credentials.py to point to your postgressql database.\ne.g. so its content is:\n```\nhostname = 'localhost'\nusername = 'xiadmin'\npassword = 'your_password_here'\ndatabase = 'xiview'\nport = 5432\n```\n\nSet up the python environment:\n\n```\ncd xiSPEC_ms_parser\npipenv install --python 3.10\n```\n\nrun create_db_schema.py to create the database tables:\n```\npython create_db_schema.py\n```\n\nparse a test dataset:\n```\npython process_dataset.py -d ~/PXD038060 -i PXD038060\n```\n\nThe argument ```-d``` is the directory to read files from and ```-i``` is the project identifier to use in the database.\n\n### To run tests\n\nMake sure we have the right db user available\n```\npsql -p 5432 -c \"create role ximzid_unittests with password 'ximzid_unittests';\"\npsql -p 5432 -c 'alter role ximzid_unittests with login;'\npsql -p 5432 -c 'alter role ximzid_unittests with createdb;'\npsql -p 5432 -c 'GRANT pg_signal_backend TO ximzid_unittests;'\n```\nrun the tests\n\n```pipenv run pytest```\n",
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