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alv

alv: a console-based viewer for molecular sequence alignments - Published in JOSS (2018)

https://github.com/arvestad/alv

Science Score: 100.0%

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

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    CITATION.cff file
    Found CITATION.cff file
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    Found codemeta.json file
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    DOI references
    Found 7 DOI reference(s) in README and JOSS metadata
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    Links to: joss.theoj.org, zenodo.org
  • ✓
    Committers with academic emails
    2 of 9 committers (22.2%) from academic institutions
  • ○
    Institutional organization owner
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    JOSS paper metadata
    Published in Journal of Open Source Software

Scientific Fields

Biology Life Sciences - 34% confidence
Last synced: 4 months ago · JSON representation ·

Repository

A console-based alignment viewer

Basic Info
  • Host: GitHub
  • Owner: arvestad
  • License: gpl-3.0
  • Language: Python
  • Default Branch: master
  • Size: 5.11 MB
Statistics
  • Stars: 116
  • Watchers: 2
  • Forks: 15
  • Open Issues: 1
  • Releases: 11
Created over 7 years ago · Last pushed 7 months ago
Metadata Files
Readme Changelog Contributing License Citation

README.md

PyPI version DOI DOI Downloads Tests Quality Gate Status

alv: a command-line alignment viewer

View your DNA or protein multiple-sequence alignments right at your command line. No need to launch a GUI!

Note: alv requires Python v3.6 or later. Earlier versions may also work, but this has not been tested.

Latest feature additions

  • If you have more than one alignment in your input file, then the first alignment is output unless you use the --alignment-index (-ai) option to choose another.
  • alv is now adapted for use in Python notebooks (tested on Jupyter) through two convenience functions 'view' and 'glimpse'. Both functions take a BioPython alignment object and outputs a view of the alignment.

Writing from Bio import AlignIO msa = AlignIO.read('PF00005.fa', 'fasta') import alv alv.view(msa) in a Jupyter notebook cell and evaluating will yield a colored alignment in the alv style.

For large alignments, the glimpse function is convenient since a subset of the alignment, selected as an easily detected conserved region, is shown. alv.glimpse(msa) Look for more usage information view help(alv.view) in a notebook cell.

Features

  • Command-line based, no GUI, so easy to script viewing of many (typically small) MSAs.
  • Reads alignments in FASTA, Clustal, PHYLIP, NEXUS, and Stockholm formats, from file or stdin.
  • Output is formatted to suit your terminal. You can also set the alignment width with option -w.
  • Can color alignments of coding DNA by codon's translations to amino acids.
  • Guesses sequence type (DNA/RNA/AA/coding) by default. You can override with option -t.
  • Order sequence explicitly, alphabetically, or by sequence similarity.
  • Restrict coloring to where you don't have indels or where there is a lot of conservation.
  • Focus on variable columns with the options --only-variable and --only-variable-excluding-indels, contributed by nikostr, that constrains coloring to columns with variation and variation not counting indels.
  • The command alv -g huge_msa.fa displays cut-out of the MSA, guaranteed to fit one terminal page without scrolling or MSA line breaking, that is supposed to give you an idea of alignment quality and contents.
  • Write alv -r 20 huge_msa.fa to get a view of the MSA containing only 20 randomly selected sequences.

Install

Recommended installation is: pip install --upgrade pip pip install alv

If you have a half-modern BioPython installed, Python v3.4 should work. BioPython is a dependency and will only get installed automatically with pip install alv if you are using Python v3.6 or later, because BioPython was apparently not on PyPi before that.

Install the commandline tool system-wide

If you would like to install the alv commandline tool system-wide, so that it is accessible regardless of which python environment you have loaded, or if you have loaded one at all, one way to do this is using the pipx installer.

After installing pipx using it's official installation instructions you can install alv with:

pipx install alv

After this, alv should be available as a command regardless of Python environment.

(Note that this only works for installing the alv commandline tool, not the Python library!)

Examples

Quick viewing of a small alignment: alv msa.fa This autodetects sequence type (AA, DNA, RNA, coding DNA), colors the sequences, and formats the alignment for easy viewing in your terminal. When applying alv to an alignment of coding DNA, the coding property is autodetected and colors are therefore applied to codons instead of nucleotides. Seven coding DNA sequences

View three sequences, accessions a, b, and c, from an alignment: alv -so a,b,c msa.fa

Feed alignment to less, for paging support. alv -k msa.fa | less -R The -k option ensures that alv keeps coloring the alignment (by default, piping and redirection removes colors), and the -R option instructs less to interpret color codes.

Choose to view a sub-alignment: alv -sa 30 60 msa.fa This selects and views columns 30 to 59 of msa.fa, keeping track of the "original" columns indexes in the output.

For developers

  • Run pip install -e . to get an "editable" install, while coding.
  • Run python -m build to prepare a distributable file.

Screenshots

Full PFAM domain

All of the sequences in PFAM's seed alignment for PF00005

PF00005 seed MSA

Yeast sequences from PF00005

Using the option -sm YEAST, we reduce the alignment to the ones with a matching accession.

Small MSA from PF00005

Owner

  • Name: Lars Arvestad
  • Login: arvestad
  • Kind: user
  • Location: Kräftriket, Stockholm
  • Company: Stockholm University

JOSS Publication

alv: a console-based viewer for molecular sequence alignments
Published
November 07, 2018
DOI
Volume 3, Issue 31, Page 955
Authors
Lars Arvestad ORCID
Department of Mathematics, Stockholm University, Sweden, Science for Life Laboratory, Solna, Sweden, Swedish e-science Research Centre
Editor
Yo Yehudi ORCID
Tags
bioinformatics console multiple sequence alignment DNA RNA protein
View PDF Review Thread Software Archive

Citation (CITATION.cff) 

cff-version: 1.1.0
message: "If you use this software, please cite it as below."
authors:
  - family-names: Arvestad
    given-names: Lars
    orcid: https://orcid.org/0000-0001-5341-1733
title: "alv: a console-based viewer for molecular sequence alignments"
version: 1.0.5
doi: https://doi.org/10.21105/joss.00955
date-released: 2018-08-12

GitHub Events

Total
  • Issues event: 1
  • Watch event: 8
  • Issue comment event: 7
  • Push event: 8
  • Pull request event: 6
  • Fork event: 1
Last Year
  • Issues event: 1
  • Watch event: 8
  • Issue comment event: 7
  • Push event: 8
  • Pull request event: 6
  • Fork event: 1

Committers

Last synced: 5 months ago

All Time
  • Total Commits: 253
  • Total Committers: 9
  • Avg Commits per committer: 28.111
  • Development Distribution Score (DDS): 0.534
Past Year
  • Commits: 16
  • Committers: 3
  • Avg Commits per committer: 5.333
  • Development Distribution Score (DDS): 0.438
Top Committers
Name Email Commits
arvestad a****e@m****e 118
arvestad a****e@c****e 109
Joon-Klaps j****s@k****e 9
Nikos Tsardakas Renhuldt n****r 6
Lars Arvestad a****e@a****e 6
SimonGreenhill s****n@s****z 2
Samuel Lampa s****a@s****e 1
Edward Davis ed@c****u 1
Lars Arvestad l****d@s****e 1
Committer Domains (Top 20 + Academic)
scilifelab.se: 2 cqls.oregonstate.edu: 1 simon.net.nz: 1 arve.math.su.se: 1 kuleuven.be: 1 csc.kth.se: 1 math.su.se: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time
  • Total issues: 17
  • Total pull requests: 20
  • Average time to close issues: about 2 months
  • Average time to close pull requests: about 13 hours
  • Total issue authors: 14
  • Total pull request authors: 6
  • Average comments per issue: 3.59
  • Average comments per pull request: 1.8
  • Merged pull requests: 18
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 6
  • Average time to close issues: about 19 hours
  • Average time to close pull requests: 1 day
  • Issue authors: 1
  • Pull request authors: 2
  • Average comments per issue: 0.0
  • Average comments per pull request: 1.5
  • Merged pull requests: 5
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • schultzm (2)
  • nikostr (2)
  • karinlag (2)
  • multimeric (1)
  • davised (1)
  • stx-tiffhu (1)
  • jrjhealey (1)
  • roey-angel (1)
  • katieemelianova (1)
  • rtviii (1)
  • SimonGreenhill (1)
  • jakobnissen (1)
  • Joon-Klaps (1)
  • camilogarciabotero (1)
Pull Request Authors
  • arvestad (13)
  • Joon-Klaps (4)
  • nikostr (3)
  • samuell (2)
  • davised (1)
  • SimonGreenhill (1)
Top Labels
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Packages

  • Total packages: 1
  • Total downloads:
    • pypi 252 last-month
  • Total dependent packages: 1
  • Total dependent repositories: 1
  • Total versions: 19
  • Total maintainers: 1
pypi.org: alv

A console-based sequence alignment viewer

  • Versions: 19
  • Dependent Packages: 1
  • Dependent Repositories: 1
  • Downloads: 252 Last month
Rankings
Dependent packages count: 4.7%
Stargazers count: 7.3%
Forks count: 10.2%
Average: 11.3%
Downloads: 12.4%
Dependent repos count: 21.7%
Maintainers (1)
arve
Last synced: 4 months ago

Dependencies

setup.py pypi
  • biopython >=1.70
  • colorama >=0.3.8