REST-like web service that provides a single endpoint gene_suggest.
The endpoint accepts the following arguments:
- query - the partial query typed by the user, e.g.
brc(as in the example above) - species - the name of the target species, e.g.
homo_sapiens - limit - the maximum number of suggestions to return, e.g.
10
If there is no any arguments enpoint use this default arguments:
- species=homo_sapiens
- label=BRC%
- limit=2
The endpoint needs for correct work following pakages:
- Click == 7.0
- Flask == 1.1.1
- Flask-Jsonpify == 1.5.0
- Flask-RESTful == 0.3.7
- Jinja2 == 2.10.1
- MarkupSafe == 1.1.1
- PyMySQL == 0.9.3
- SQLAlchemy == 1.3.8
- Werkzeug == 0.16.0
- aniso8601 == 8.0.0
- itsdangerous == 1.1.0
- pip == 19.0.3
- pytz == 2019.2
- setuptools == 40.8.0
- six == 1.12.0
Please use this or next version of packages. It also provides venv package for fast run.
Examples:
{a}: http://127.0.0.1:5000/gene_suggest - default search
{b}: http://127.0.0.1:5000/gene_suggest?species=homo_sapiens&label=BRC%%&limit=2 - default parametrs
{c}: http://127.0.0.1:5000/gene_suggest?species=homo_sapiens&label=BRCA1&limit=2
{d}: http://127.0.0.1:5000/gene_suggest?species=homo_sapiens&label=BRCC3P1&limit=2
Note: You can use regular expression in label but you should use %% instead % for correct processing SQL-query. Please check, you IP may be 0.0.0.0 instead of 127.0.0.1 it depends on your OS.
Output: json-file with gene data
Output for examples:
{a}: {"search": [{"species": "homo_sapiens", "stable_id": "ENSG00000012048", "display_label": "BRCA1", "location": "17:43044295-43170245", "db": "core"}, {"species": "homo_sapiens", "stable_id": "ENSG00000139618", "display_label": "BRCA2", "location": "13:32315474-32400266", "db": "core"}]}
{b}: {"search": [{"species": "homo_sapiens", "stable_id": "ENSG00000012048", "display_label": "BRCA1", "location": "17:43044295-43170245", "db": "core"}, {"species": "homo_sapiens", "stable_id": "ENSG00000139618", "display_label": "BRCA2", "location": "13:32315474-32400266", "db": "core"}]}
{c}: {"search": [{"species": "homo_sapiens", "stable_id": "ENSG00000012048", "display_label": "BRCA1", "location": "17:43044295-43170245", "db": "core"}]}
{d}: {"search": [{"species": "homo_sapiens", "stable_id": "ENSG00000251667", "display_label": "BRCC3P1", "location": "5:176308063-176309013", "db": "core"}]}