One post tagged with "exome"

In an effort to make it easier for our users to connect with the existing tools in their stack, we're excited to announce that Exome now supports communicating over the Postgres wire protocol. What this means is that users can use psql in the console or psycopg2 to connect to Exome and query their data.

To be clear, Exome does not yet support the pg_catalog system catalog, meaning that many BI dashboard and ETL tools will not work with Exome yet. However, we're working on adding support for pg_catalog and hope to have it available soon.

Connecting to Exome with psql​

Assuming you've made an Exome user, you can connect the example catalog in Exome with psql using the following command:

psql -W -H pg.exome.wheretrue.com -U test@mail.com -d public.example_library.example_catalog

If that all goes well, you'll be prompted for your password and then connected to the Exome catalog. You can then run queries as you would with any other Postgres database.

$ psql -W -H pg.exome.wheretrue.com -U test@mail.com -d public.example_library.example_catalog
psql (14.9 (Homebrew), server 0.1.0)
SSL connection (protocol: TLSv1.3, cipher: TLS_AES_256_GCM_SHA384, bits: 256, compression: off)
Type "help" for help.

public.example_library.example_catalog=>

We can then run queries as we would with any other Postgres database.

public.example_library.example_catalog=> SELECT COUNT(*) FROM example_catalog.example_schema.fasta_table;
 cnt
-----
 500
(1 row)

public.example_library.example_catalog=> SELECT id, description FROM example_catalog.example_schema.fasta_table LIMIT 5;
         id          |                                                description
---------------------+-----------------------------------------------------------------------------------------------------------
 UniRef50_A0A5A9P0L4 | peptidylprolyl isomerase n=1 Tax=Triplophysa tibetana TaxID=1572043 RepID=A0A5A9P0L4_9TELE
 UniRef50_A0A410P257 | Glycogen synthase n=2 Tax=Candidatus Velamenicoccus archaeovorus TaxID=1930593 RepID=A0A410P257_9BACT
 UniRef50_A0A8J3NBY6 | Gln_amidase domain-containing protein n=2 Tax=Actinocatenispora rupis TaxID=519421 RepID=A0A8J3NBY6_9ACTN
 UniRef50_Q8WZ42     | Titin n=3053 Tax=cellular organisms TaxID=131567 RepID=TITIN_HUMAN
 UniRef50_A0A401TRQ8 | Ig-like domain-containing protein (Fragment) n=2 Tax=Chiloscyllium TaxID=34767 RepID=A0A401TRQ8_CHIPU

Connect to Exome with psycopg2​

psycopg2 is a popular Python library for connecting to Postgres databases. It's used by many Python libraries and frameworks, including Django and SQLAlchemy. To connect to Exome with psycopg2, you'll need to install the psycopg2 package in your python environment.

pip install psycopg2

Once you've installed psycopg2, you can connect to Exome with the following code:

import psycopg2

conn = psycopg2.connect(
    host="pg.exome.wheretrue.com",
    port=5432,
    user="user@example.com",
    password="RainbowsAndUnicorns",
    dbname="public.example_library.example_catalog",
)

conn.autocommit = True

cur = conn.cursor()
cur.execute("SELECT COUNT(*) cnt FROM example_catalog.example_schema.fasta_table;")
print(cur.fetchone())

If that all goes well, you should see the following output:

(500,)

What's Next?​

We're working on adding support for pg_catalog and hope to have it available soon. If you have any questions or feedback, please reach out to us at support@wheretrue.com.

Signup for Exome to try it for yourself.