https://github.com/edinburgh-genome-foundry/icebreaker
:snowflake: Python API for the JBEI-ICE sample manager
https://github.com/edinburgh-genome-foundry/icebreaker
jbei-ice lab-automation sample-management synthetic-biology
Last synced: 5 months ago
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:snowflake: Python API for the JBEI-ICE sample manager
- Host: GitHub
- URL: https://github.com/edinburgh-genome-foundry/icebreaker
- Owner: Edinburgh-Genome-Foundry
- License: other
- Created: 2018-09-16T18:39:48.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2020-09-29T15:15:15.000Z (over 4 years ago)
- Last Synced: 2024-11-09T08:49:28.659Z (6 months ago)
- Topics: jbei-ice, lab-automation, sample-management, synthetic-biology
- Language: Python
- Homepage: https://edinburgh-genome-foundry.github.io/icebreaker/
- Size: 1.7 MB
- Stars: 6
- Watchers: 4
- Forks: 1
- Open Issues: 1
-
Metadata Files:
- Readme: README.rst
Awesome Lists containing this project
README
IceBreaker
----------
..
.. image:: https://travis-ci.org/Edinburgh-Genome-Foundry/icebreaker.svg?branch=master
:target: https://travis-ci.org/Edinburgh-Genome-Foundry/icebreaker
.. image:: https://coveralls.io/repos/github/Edinburgh-Genome-Foundry/icebreaker/badge.svg?branch=master
:target: https://coveralls.io/github/Edinburgh-Genome-Foundry/icebreaker?branch=master
Icebreaker provides a Python interface for the `JBEI ICE sample manager `_.
See the full API documentation `here `_
Installation
-------------
Icebreaker is written for Python 3+. You can install icebreaker via PIP:
.. code::
sudo pip install icebreaker
Alternatively, you can unzip the sources in a folder and type
.. code::
sudo python setup.py install
Example of use
---------------
In this example we assume that we are a lab who wants to find primers from its
database to sequence a given construct. We will (1) pull all our primers from
ICE, (2) find which primers are adapted to our sequence, using the
`Primavera package `_, and
(3) we will ask ICE for the location of the selected primers.
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.
.. code:: python
import icebreaker
# CONNECT TO ICE
configuration = dict(
root="https://my.ice.instance.org",
token="WMnlYlWHz+BC+7eFV=...",
client = "icebot"
)
ice = icebreaker.IceClient(configuration)
Or:
.. code:: python
# CONNECT TO ICE
configuration = dict(
root="https://my.ice.instance.org",
email="[email protected]",
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:
.. code:: yaml
root: https://my.ice.instance.org
email: [email protected]
password: ic3ic3baby
Extracting all records from a folder
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Next we pull all primers in the database:
.. code:: python
# 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 `_):
.. code:: python
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:
.. code:: python
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:
.. code:: bash
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.
Getting an ICE token
--------------------
There are several ways to get ICE tokens. We suggest you create one throug
the web interface as follows (see screenshot for indications):
0. Create an account with administrator rights
1. Go to the administrator panel
2. Click on "API keys"
3. Click on "create new". Note everything down !
.. image:: https://github.com/Edinburgh-Genome-Foundry/icebreaker/raw/master/docs/_static/api_key_screenshot.png
:alt: screenshot
:align: center
License = MIT
--------------
Icebreaker is an open-source software originally written at the Edinburgh
Genome Foundry by `Zulko `_ and `released on
Github `_ under
the MIT licence (Copyright Edinburg Genome Foundry). Everyone is welcome to
contribute !
More biology software
-----------------------
.. image:: https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/Edinburgh-Genome-Foundry.github.io/master/static/imgs/logos/egf-codon-horizontal.png
:target: https://edinburgh-genome-foundry.github.io/
Icebreaker is part of the `EGF Codons `_ synthetic biology software suite for DNA design, manufacturing and validation.