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easyalign

Python Implementation of classic local and global alignment algorithms

https://github.com/jamesdconley/easyalign

Science Score: 10.0%

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

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 1 committers (100.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (5.5%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Python Implementation of classic local and global alignment algorithms

Basic Info
  • Host: GitHub
  • Owner: JamesDConley
  • License: mit
  • Language: Python
  • Default Branch: master
  • Size: 5.86 KB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created over 7 years ago · Last pushed almost 6 years ago

https://github.com/JamesDConley/EasyAlign/blob/master/ 

# EasyAlign
This software can align python lists of any objects that can be compared with the '==' operator (strings, floats, whatever!)

## Getting started
The easiest way to install is with pip!

`pip install EasyAlign` 


## Usage

```
from EasyAlign import LocalAligner, GlobalAligner
seq1 = [5,  1, 2, 3, 4, 5]
seq2 = [5, 1, 1,  1, 1, 1, 2, 3]
my_local_aligner = LocalAligner(2, -1)
aligned_seq1,  aligned_seq2,  score = my_local_aligner.align(seq1, seq2)
print(aligned_seq1,  aligned_seq2,  score )
my_global_aligner = GlobalAligner(2, -1)
aligned_seq1,  aligned_seq2,  score = my_global_aligner.align(seq1, seq2)
print(aligned_seq1,  aligned_seq2,  score )
```

If you want to look at more local alignments than just the best scored one you can directly access the score table from the last alignment using my_local_aligner.table - it's a 2d list of integers.  You can then pass the x,y coordinates (seq1 is x, seq2 is y) to my_local_aligner.traceback(x,y) which will return the aligned local sequences that end at that x/y coord.

## Thank You!
Thanks for using EasyAlign! :)

Owner

  • Name: James Conley
  • Login: JamesDConley
  • Kind: user

Data Scientist at SFL Scientific (Personal Account)

GitHub Events

Total
Last Year

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 7
  • Total Committers: 1
  • Avg Commits per committer: 7.0
  • Development Distribution Score (DDS): 0.0
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
James Conley j****1@c****u 7
Committer Domains (Top 20 + Academic)
conncoll.edu: 1

Issues and Pull Requests

Last synced: about 1 year ago

All Time
  • Total issues: 0
  • Total pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Total issue authors: 0
  • Total 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
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
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Top Labels
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Packages

  • Total packages: 1
  • Total downloads:
    • pypi 11 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 1
  • Total maintainers: 1
pypi.org: easyalign

Simple Python Implementation of the Smith-Waterman and Needleman-Wunsch Algorithms

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 11 Last month
Rankings
Dependent packages count: 10.0%
Dependent repos count: 21.7%
Forks count: 29.8%
Average: 30.0%
Stargazers count: 38.8%
Downloads: 49.5%
Maintainers (1)
JamesDonConley
Last synced: 10 months ago

Dependencies

setup.py pypi
  • beautifulsoup4 *
  • get *
  • validators *