Connexion to an ICE instance

You can connecct to your ICE instance using either an API token (see below for how to create a token), or an email/password authentication.

import icebreaker

# CONNECT TO ICE
configuration = dict(
    root="https://my.ice.instance.org",
    token="WMnlYlWHz+BC+7eFV=...",
    client = "icebot"
)
ice = icebreaker.IceClient(configuration)

Or:

# CONNECT TO ICE
configuration = dict(
    root="https://my.ice.instance.org",
    email="michael.swann@genomefoundry.org",
    password = "ic3ic3baby"
)
ice = icebreaker.IceClient(configuration)

The configuration can also be written in a yaml file so you can write IceClient('config.yml') where config.yml reads as follows:

root: https://my.ice.instance.org
email: michael.swann@genomefoundry.org
password: ic3ic3baby

Extracting all records from a folder

Next we pull all primers in the database:

# FIND THE ID OF THE FOLDER WITH ALL PRIMERS
primers_folder = ice.get_folder_id("PRIMERS", collection="SHARED")

# GET INFOS ON ALL ENTRIES IN THE FOLDER (PRIMER NAME, ID, CREATOR...)
primers_entries = ice.get_folder_entries(primers_folder)

# GET A BIOPYTHON RECORD FOR EACH PRIMER
primers_records = {primer["id"]: ice.get_record(primer["id"])
                   for primer in primers_entries}

Primer selection with Primavera

Next provide this information to Primavera and select some primers (see the Primavera docs):

from primavera import PrimerSelector, Primer, load_record

available_primers = [
    Primer(sequence=primers_records[entry['id']].seq.tostring(),
        name=entry['name'],
        metadata=dict(ice_id=entry['id']))
    for entry in primers_entries
]
constructs = [load_record("RTM3_39.gb", linear=False)]
selector = PrimerSelector(read_range=(150, 1000), tm_range=(55, 70),
                        size_range=(16, 25), coverage_resolution=10,
                        primer_reuse_bonus=200)
selected_primers = selector.select_primers(constructs, available_primers)

Finding available samples

Finally we look for available samples for each primer:

selected_primers = set(sum(selected_primers, []))
for primer in selected_primers:
    ice_id = primer.metadata.get("ice_id", None)
    if ice_id is not None:
        samples = ice.get_samples(ice_id)
        if len(samples) > 0:
            location = icebreaker.sample_location_string(samples[0])
            print("Primer %s is in %s." % (primer.name, location))

Result:

Primer PRV_EMMA_IN00042 is in PRIMER_PLATE_1/E06.
Primer PRV_EMMA_IN00043 is in PRIMER_PLATE_1/F06.
Primer PRV_EMMA_IN00028 is in PRIMER_PLATE_1/G04.
Primer PRV_EMMA_IN00060 is in PRIMER_PLATE_1/G08.
Primer PRV_EMMA_IN00064 is in PRIMER_PLATE_1/C09.
Primer PRV_EMMA_IN00038 is in PRIMER_PLATE_1/A06.
Primer PRV_EMMA_IN00068 is in PRIMER_PLATE_1/G09.