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apollo-4.2.9
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مشاهده بیشترتوضیحات
Apollo API library
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | apollo-4.2.9 |
| نام | apollo |
| نسخه کتابخانه | 4.2.9 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Helena Rasche;Anthony Bretaudeau;Nathan Dunn |
| ایمیل نویسنده | hxr@hx42.org |
| آدرس صفحه اصلی | https://github.com/galaxy-genome-annotation/python-apollo |
| آدرس اینترنتی | https://pypi.org/project/apollo/ |
| مجوز | MIT |
Apollo API Library
==================
.. image:: https://travis-ci.org/galaxy-genome-annotation/python-apollo.svg?branch=master
:target: https://travis-ci.org/galaxy-genome-annotation/python-apollo
.. image:: https://readthedocs.org/projects/python-apollo/badge/?version=latest
:target: http://python-apollo.readthedocs.io/en/latest/?badge=latest
:alt: Documentation Status
Apollo is a Python library for interacting with
`Apollo <https://github.com/gmod/apollo/>`__. Arrow is its companion CLI tool.
`for the record <https://gitter.im/galaxy-genome-annotation/Lobby?at=5ebee6c049a1b7318479380d>`__ ... arrow makes working with Apollo SOOO much easier
— Nathan Dunn, Apollo Developer
Installation
------------
.. code-block:: shell
pip install apollo
Examples
--------
Example code to create a new organism and add yourself in the permission list:
.. code:: python
from apollo import ApolloInstance
wa = ApolloInstance('https://fqdn/apollo', 'jane.doe@fqdn.edu', 'password')
orgs = wa.organisms.add_organism(
"Yeast",
"/path/to/jbrowse/data",
genus='Saccharomyces',
species='cerevisiae',
public=False
)
# Give Apollo a second to process the uploaded organism.
time.sleep(1)
# Then add yourself to permission list
data = wa.users.update_organism_permissions(
"jane.doe@fqdn.edu",
"Yeast",
write=True,
export=True,
read=True,
)
If you have already created an Arrow config file (with command `arrow init`),
you can also get an ApolloInstance without writing credentials explicitely:
.. code:: python
from arrow.apollo import get_apollo_instance
wa = get_apollo_instance()
Or with the Arrow client:
.. code-block:: shell
$ arrow groups create_group university
{
"publicGroup": false,
"class": "org.bbop.apollo.UserGroup",
"name": "university",
"users": null,
"id": 558319
}
# THEN
$ arrow users get_users | \
jq '.[] | select(.username | contains("@tamu.edu")) | .username' | \
xargs -n1 arrow users add_to_group university
# OR
$ arrow users get_users | \
jq '.[] | select(.username | contains("@tamu.edu")) | .username' | \
paste -s -d',' | \
xargs arrow group update_membership 558319 --users
History
-------
- 4.2.13
- Relax biopython requirements
- 4.2.12
- Do not filter out username from api responses
- 4.2.11
- Updated wrong version number
- 4.2.10
- Bugfix handling Shine-Dalgarno sequences (https://github.com/galaxy-genome-annotation/python-apollo/issues/48)
- 4.2.9
- Bugfix to update_organism when using suppress_output
- 4.2.8
- Added --suppress_output to update_organism
- 4.2.7
- Renamed --return_all option to --suppress_output
- 4.2.6
- Added --return_all option to add_organism and delete_organism methods
- 4.2.5
- Prevent from displaying login/password in the logs
- 4.2.4
- Remove unused dependency
- 4.2.3
- Fixed `load_gff3` to more accurately load transcripts including the CDS as well as handle non-coding types more accurately.
- 4.2.2
- Drastically speed up load_gff3
- `load_gff3` now uses the Apollo `add_transcript` method if it is a gene or mRNA type
- Added support for all of the current Apollo coding and non-coding types
- Drop support for Python 2.7
- 4.2.1
- Fix getting groups by name
- Add tests for group api
- 4.2
- Improve user update method
- Add tests for user api
- 4.1
- Fix loading attributes from gff3
- Better handling of genome sequence update, with or without the no_reload_sequences option
- 4.0.1
- Fix missing file in pypi package, no code change
- 4.0
- Added support for remote creation/update/deletion of organisms/tracks
- Added support for adding GFF3 in the annotation track
- Added tests
- 3.1
- Added user activate/inactivate
- Added get_creator for user, group and organisms
- Added omitEmptyOrganisms to get_users
- Added support for group admins
- Added support for bulk group creation/deletion
- Repaired GFF3/Fasta downloading
- 3.0.4
- `Fixed bug <https://github.com/galaxy-genome-annotation/python-apollo/issues/4>`__ in deleteFeatures (Thanks `@NeillGibson <https://github.com/NeillGibson>`__)
- 3.0.3
- findAllOrganisms works correctly, client side filtering no longer necessary.
- 3.0.2
- Patch a bug discovered in io.write, thanks Morgan!
- 3.0
- "Arrow" CLI utility
- More pythonic API and many workarounds for Apollo bugs or oddities
- Complete package restructure
- Nearly all functions renamed
- 2.0
- Galaxy Functions
- TTL Cache to work around Galaxy's behaviour
- Status and Canned* Clients from `@abretaud <https://github.com/abretaud>`__
- 1.0
- Initial release
Development
-----------
The content of docs and arrow directories is automatically generated from the code in the apollo directory.
To regenerate it, install the latest version of the code, then run:
.. code-block:: shell
make rebuild
License
-------
Available under the MIT License
Support
-------
This material is based upon work supported by the National Science Foundation under Grant Number (Award 1565146)
نیازمندی
| مقدار | نام |
|---|---|
| - | requests |
| >=1.77 | biopython |
| <4 | cachetools |
| >=6.7 | click |
| - | wrapt |
| - | pyyaml |
| - | decorator |
| >=0.6.6 | bcbio-gff |
نحوه نصب
نصب پکیج whl apollo-4.2.9:
pip install apollo-4.2.9.whl
نصب پکیج tar.gz apollo-4.2.9:
pip install apollo-4.2.9.tar.gz