alignmentrs
Quickly read and manipulate multiple sequence alignments in Python
Installation
pip install alignmentrs
Quickstart
Import alignment into Python
>>> import alignmentrs as rs
>>> aln = rs.Alignment.from_fasta('hiv.fna', 'HIV_alignment')
>>> aln
Alignment(nsamples=10, nsites=120, nmarkers=0)
>>> aln.sample_ids
['sample01', 'sample02', 'sample03', 'sample04', 'sample05', 'sample06'
'sample07', 'sample08', 'sample09', 'sample10']
Select sites to remove from the alignment
>>> sites_to_remove = [i for i in range(120) if (i-2) % 3 != 0] # remove 1st and 2nd position in codon triplet
>>> aln.remove_sites(sites_to_remove, copy=False) # manipulate inplace, copy=True returns a new copy
Alignment(nsamples=10, nsites=40, nmarkers=0)
Select sites to retain in the alignment
>>> sites_to_retain = list(range(2, 3, 120)) # third position in codon triplet
>>> aln.retain_sites(sites_to_retain, copy=False) # manipulate inplace, copy=True returns a new copy
Alignment(nsamples=10, nsites=40, nmarkers=0)
Get a subset of samples and sites
>>> sub_aln = aln.subset(samples=['sample01', 'sample03', 'sample05'], sites=list(range(2, 3, 120)))
>>> sub_aln
Alignment(nsamples=3, nsites=40, nmarkers=0)
License
1 maintainer
Metadata
1 maintainer
Release files for alignmentrs 0.9.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Built distributions (wheels)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| alignmentrs-0.9.0-cp37-cp37m-macosx_10_7_x86_64.whl | CPython 3.7 | CPython 3.7 pymalloc | macOS 10.7+ x86-64 | Details |
| alignmentrs-0.9.0-cp36-cp36m-macosx_10_7_x86_64.whl | CPython 3.6 | CPython 3.6 pymalloc | macOS 10.7+ x86-64 | Details |
| alignmentrs-0.9.0-cp35-cp35m-macosx_10_5_x86_64.whl | CPython 3.5 | CPython 3.5 pymalloc | macOS 10.5+ x86-64 | Details |
Total release size: 11.5 MB
Release files / alignmentrs-0.9.0-cp37-cp37m-macosx_10_7_x86_64.whl
| Download URL | alignmentrs-0.9.0-cp37-cp37m-macosx_10_7_x86_64.whl |
|---|---|
| Size | 5.8 MB |
| Tags | CPython 3.7 CPython 3.7 pymalloc macOS 10.7+ x86-64 |
|
SHA-256 checksum How to use checksums |
26625d18107baf620a6e7f76384a092d7526b66c56487f5aed2d5bde83b12cfd
|
|
BLAKE2b-256 checksum How to use checksums |
5631f12e65163a7530f385c3cd399770e93eb3e752cc9154dd9ab4090133af77
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/1.12.1 pkginfo/1.5.0.1 requests/2.21.0 setuptools/40.6.3 requests-toolbelt/0.8.0 tqdm/4.30.0 CPython/3.7.2
|
Release files / alignmentrs-0.9.0-cp36-cp36m-macosx_10_7_x86_64.whl
| Download URL | alignmentrs-0.9.0-cp36-cp36m-macosx_10_7_x86_64.whl |
|---|---|
| Size | 3.9 MB |
| Tags | CPython 3.6 CPython 3.6 pymalloc macOS 10.7+ x86-64 |
|
SHA-256 checksum How to use checksums |
476ed6d3ef40023efef3dc5d134f2fe89c5c41fadf411e502d633e10dc43ff40
|
|
BLAKE2b-256 checksum How to use checksums |
cb2b1bafcf86da63f8f46513c537cc550a051d5846649d4ba0229294fd6f8526
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/1.12.1 pkginfo/1.5.0.1 requests/2.21.0 setuptools/40.6.3 requests-toolbelt/0.8.0 tqdm/4.30.0 CPython/3.7.2
|
Release files / alignmentrs-0.9.0-cp35-cp35m-macosx_10_5_x86_64.whl
| Download URL | alignmentrs-0.9.0-cp35-cp35m-macosx_10_5_x86_64.whl |
|---|---|
| Size | 1.9 MB |
| Tags | CPython 3.5 CPython 3.5 pymalloc macOS 10.5+ x86-64 |
|
SHA-256 checksum How to use checksums |
268a327d9e1db42c0e606b5b76f4e075e42285a61e2adb9889e7c8b57db88bb3
|
|
BLAKE2b-256 checksum How to use checksums |
645467e4dbccdd96571885ded23abdb0e59d1bd174ce657f54adb64472146d52
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/1.12.1 pkginfo/1.5.0.1 requests/2.21.0 setuptools/40.6.3 requests-toolbelt/0.8.0 tqdm/4.30.0 CPython/3.7.2
|
Security for alignmentrs 0.9.0
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.
