# swalign
This package implements a Smith-Waterman style local alignment algorithm. You can align a query sequence to a reference. The scoring functions can be based on a matrix, or simple identity. Weights can be adjusted for match/mismatch and gaps, with gap extention penalties. Additionally, the gap penalty can be subject to a decay to prioritize long gaps.
The input files are FASTA format sequences, or strings of sequences.
Here is some skeleton code to get you started:
import swalign # choose your own values here… 2 and -1 are common. match = 2 mismatch = -1 scoring = swalign.NucleotideScoringMatrix(match, mismatch)
sw = swalign.LocalAlignment(scoring) # you can also choose gap penalties, etc… alignment = sw.align(‘ACACACTA’,’AGCACACA’) alignment.dump()
For other uses, see the script in bin/swalign or https://compgen.io/projects/swalign
1 maintainer
Metadata
1 maintainer
Release files for swalign 0.3.7
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | Provenance | Actions |
|---|---|---|---|---|
| swalign-0.3.7.tar.gz | 7.8 kB | Without provenance | Details for swalign-0.3.7.tar.gz |
Release files / swalign-0.3.7.tar.gz
| Download URL | swalign-0.3.7.tar.gz |
|---|---|
| Size | 7.8 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
de9607564996ae877fdabd7f305b1acfa8bc70556c4d40a40cf0915a4a560289
|
|
BLAKE2b-256 checksum How to use checksums |
ca5aad32a28285cf9046b7eea9978e7e8c6a1fbadbe71b9ccfa4db60ef06dbb7
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
Python-urllib/3.6
|
Security for swalign 0.3.7
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
No provenance found
None of the files in this release were uploaded with provenance metadata.
A note on package security
PyPI is a repository for distributing packages, not a service for auditing them. While third-party security researchers and our staff do their best to detect and remove malicious packages, PyPI cannot guarantee the quality, security or suitability of any given package.
To learn more about protecting yourself from malicious actors, visit our package security documentation.
