polya

Automatically Adjudicate Any And All Arbitrary Annotations, Astutely Adjoin Abutting Alignments, And Also Amputate Anything Amiss (AAAAAAAAAAAAAAAA)

https://github.com/traviswheelerlab/polya

Science Score: 10.0%

This score indicates how likely this project is to be science-related based on various indicators:

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CITATION.cff file
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codemeta.json file
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.zenodo.json file
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DOI references
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Academic publication links
✓
Committers with academic emails
1 of 8 committers (12.5%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (4.4%) to scientific vocabulary

Keywords

bioinformatics competing-annotations confidence-calculations sequence-alignment

Keywords from Contributors

interactive serializer cycles packaging network-simulation shellcodes hacking autograding observability genomics

Last synced: 6 months ago · JSON representation

Repository

Automatically Adjudicate Any And All Arbitrary Annotations, Astutely Adjoin Abutting Alignments, And Also Amputate Anything Amiss (AAAAAAAAAAAAAAAA)

Basic Info

Host: GitHub
Owner: TravisWheelerLab
License: bsd-3-clause
Language: Python
Default Branch: master
Homepage: https://polya.readthedocs.io/en/latest/
Size: 59 MB

Statistics

Stars: 8
Watchers: 5
Forks: 2
Open Issues: 9
Releases: 8

Topics

bioinformatics competing-annotations confidence-calculations sequence-alignment

Created about 6 years ago · Last pushed almost 2 years ago

Metadata Files

Readme License Authors

AAAAAAAAAAAAAAAA (PolyA):

Automatically Adjudicate Any And All Arbitrary Annotations, Astutely Adjoin Abutting Alignments, And Also Amputate Anything Amiss

A tool for adjudicating between competing annotations of biological sequences.

--> NOTE: PolyA is deprecated, in favor of a re-implementation of the underlying methods: AURORA <--

About

PolyA is a software tool that adjudicates between competing alignment-based annotations. PolyA communicates annotation certainty, identifies large scale rearrangements, and detects boundaries between neighboring elements.

See the documentation for more information.

License

BSD license. See LICENSE.

Authors

Wheeler Lab at the University of Montana.

Kaitlin Carey
Audrey Shingleton
George Lesica
Jack Roddy
Travis Wheeler

Owner

Name: Wheeler Lab
Login: TravisWheelerLab
Kind: organization
Email: twheeler@arizona.edu

Website: http://wheelerlab.org
Repositories: 20
Profile: https://github.com/TravisWheelerLab

GitHub Events

Total

Watch event: 1

Last Year

Watch event: 1

Committers

Last synced: over 2 years ago

All Time

Total Commits: 227
Total Committers: 8
Avg Commits per committer: 28.375
Development Distribution Score (DDS): 0.555

Past Year

Commits: 8
Committers: 1
Avg Commits per committer: 8.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
George Lesica	g**e@l**m	101
Kaitin Carey	k**y@u**u	64
Audrey Shingleton	a**8@i**m	30
Kaitlin Carey	3****y	15
Jack Roddy	j**y@g**m	8
Travis Wheeler	t**s@t**m	6
dependabot[bot]	4****]	2
kmcarey	k**y@o**n	1

Committer Domains (Top 20 + Academic)

oredigger.localdomain: 1 traviswheeler.com: 1 umconnect.umt.edu: 1 lesica.com: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 19
Total pull requests: 81
Average time to close issues: 11 months
Average time to close pull requests: 11 days
Total issue authors: 5
Total pull request authors: 6
Average comments per issue: 0.16
Average comments per pull request: 0.12
Merged pull requests: 69
Bot issues: 0
Bot pull requests: 7

Past Year

Issues: 0
Pull requests: 0
Average time to close issues: N/A
Average time to close pull requests: N/A
Issue authors: 0
Pull request authors: 0
Average comments per issue: 0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

glesica (15)
kmcarey (1)
Audreym98 (1)
jebrosen (1)
jackroddy (1)

Pull Request Authors

glesica (36)
Audreym98 (16)
kmcarey (15)
dependabot[bot] (7)
jackroddy (6)
traviswheeler (2)

Top Labels

Issue Labels

question (5) testing (5) dfam (4) bug (3) enhancement (3) performance (3) interface (3) documentation (3) algorithms (2)

Pull Request Labels

enhancement (12) documentation (9) dependencies (8) bug (5) testing (5) performance (4) interface (3) algorithms (1) dfam (1)

Packages

Total packages: 1
Total downloads:
- pypi 20 last-month

Total dependent packages: 0
Total dependent repositories: 1
Total versions: 9
Total maintainers: 2

pypi.org: polya

PolyA is a sequence annotation adjudicator.

Homepage: https://github.com/TravisWheelerLab/polyA
Documentation: https://polya.readthedocs.io/
License: BSD License
Latest release: 1.3.2
published almost 3 years ago

Versions: 9
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 20 Last month

Rankings

Dependent packages count: 10.0%

Forks count: 19.1%

Stargazers count: 19.3%

Average: 20.1%

Dependent repos count: 21.7%

Downloads: 30.3%

Maintainers (2)

jackroddy traviswheeler

Last synced: 6 months ago

Dependencies

Pipfile pypi

black * develop
flit * develop
ipython * develop
mypy * develop
pylint >=2.4.4,<3.0.0 develop
pytest >=5.3.5,<6.0.0 develop
scalene * develop
sphinx * develop

Pipfile.lock pypi

alabaster ==0.7.12 develop
astroid ==2.11.5 develop
attrs ==21.4.0 develop
babel ==2.10.1 develop
backcall ==0.2.0 develop
black ==22.3.0 develop
certifi ==2022.5.18.1 develop
charset-normalizer ==2.0.12 develop
click ==8.1.3 develop
cloudpickle ==2.1.0 develop
commonmark ==0.9.1 develop
decorator ==5.1.1 develop
dill ==0.3.5.1 develop
docutils ==0.18.1 develop
flit ==3.7.1 develop
flit-core ==3.7.1 develop
idna ==3.3 develop
imagesize ==1.3.0 develop
importlib-metadata ==4.11.4 develop
ipython ==7.34.0 develop
isort ==5.10.1 develop
jedi ==0.18.1 develop
jinja2 ==3.1.2 develop
lazy-object-proxy ==1.7.1 develop
markupsafe ==2.1.1 develop
matplotlib-inline ==0.1.3 develop
mccabe ==0.7.0 develop
more-itertools ==8.13.0 develop
mypy ==0.960 develop
mypy-extensions ==0.4.3 develop
numpy ==1.21.6 develop
nvidia-ml-py ==11.515.48 develop
packaging ==21.3 develop
parso ==0.8.3 develop
pathspec ==0.9.0 develop
pexpect ==4.8.0 develop
pickleshare ==0.7.5 develop
platformdirs ==2.5.2 develop
pluggy ==0.13.1 develop
prompt-toolkit ==3.0.29 develop
ptyprocess ==0.7.0 develop
py ==1.11.0 develop
pygments ==2.12.0 develop
pylint ==2.14.0 develop
pyparsing ==3.0.9 develop
pytest ==5.4.3 develop
pytz ==2022.1 develop
requests ==2.27.1 develop
rich ==12.4.4 develop
scalene ==1.5.4 develop
setuptools ==62.3.2 develop
snowballstemmer ==2.2.0 develop
sphinx ==5.0.1 develop
sphinxcontrib-applehelp ==1.0.2 develop
sphinxcontrib-devhelp ==1.0.2 develop
sphinxcontrib-htmlhelp ==2.0.0 develop
sphinxcontrib-jsmath ==1.0.1 develop
sphinxcontrib-qthelp ==1.0.3 develop
sphinxcontrib-serializinghtml ==1.1.5 develop
tomli ==2.0.1 develop
tomli-w ==1.0.0 develop
tomlkit ==0.11.0 develop
traitlets ==5.3.0.dev0 develop
typed-ast ==1.5.4 develop
typing-extensions ==4.2.0 develop
urllib3 ==1.26.9 develop
wcwidth ==0.2.5 develop
wrapt ==1.14.1 develop
zipp ==3.8.0 develop

requirements.txt pypi

Babel ==2.10.1
Jinja2 ==3.1.2
MarkupSafe ==2.1.1
Pygments ==2.12.0
Sphinx ==5.0.1
alabaster ==0.7.12
appnope ==0.1.3
astroid ==2.11.5
asttokens ==2.0.5
attrs ==21.4.0
backcall ==0.2.0
black ==22.3.0
certifi ==2022.5.18.1
charset-normalizer ==2.0.12
click ==8.1.3
cloudpickle ==2.1.0
colorama ==0.4.4
commonmark ==0.9.1
decorator ==5.1.1
dill ==0.3.5.1
docutils ==0.18.1
executing ==0.8.3
flit ==3.7.1
flit_core ==3.7.1
idna ==3.3
imagesize ==1.3.0
importlib-metadata ==4.11.4
ipython ==7.34.0
isort ==5.10.1
jedi ==0.18.1
lazy-object-proxy ==1.7.1
matplotlib-inline ==0.1.3
mccabe ==0.7.0
more-itertools ==8.13.0
mypy ==0.960
mypy-extensions ==0.4.3
numpy ==1.21.6
nvidia-ml-py ==11.515.48
packaging ==21.3
parso ==0.8.3
pathspec ==0.9.0
pexpect ==4.8.0
pickleshare ==0.7.5
platformdirs ==2.5.2
pluggy ==0.13.1
prompt-toolkit ==3.0.29
ptyprocess ==0.7.0
pure-eval ==0.2.2
py ==1.11.0
pylint ==2.14.0
pynvml ==11.4.1
pyparsing ==3.0.9
pytest ==5.4.3
pytz ==2022.1
regex ==2021.8.28
requests ==2.27.1
rich ==12.4.4
scalene ==1.5.4
six ==1.16.0
snowballstemmer ==2.2.0
sphinxcontrib-applehelp ==1.0.2
sphinxcontrib-devhelp ==1.0.2
sphinxcontrib-htmlhelp ==2.0.0
sphinxcontrib-jsmath ==1.0.1
sphinxcontrib-qthelp ==1.0.3
sphinxcontrib-serializinghtml ==1.1.5
stack-data ==0.2.0
toml ==0.10.2
tomli ==2.0.1
tomli_w ==1.0.0
tomlkit ==0.11.0
traitlets ==5.3.0.dev0
typing_extensions ==4.2.0
urllib3 ==1.26.9
wcwidth ==0.2.5
wrapt ==1.14.1
zipp ==3.8.0

.github/workflows/polyA-ci.yml actions

actions/checkout v1 composite

Dockerfile docker

python 3.7-slim-bullseye build

pyproject.toml pypi

polya

Science Score: 10.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

AAAAAAAAAAAAAAAA (PolyA):

About

License

Authors

Owner

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

pypi.org: polya

Rankings

Maintainers (2)

Dependencies