msa4u 0.4.0

A tool for short uORF annotation.

Description

MSA4u is a simple visualisation tool for Multiple Sequence Alignments.

Programming language: Python3
OS: MacOS, Linux
Python dependencies: biopython, configs, argparse, reportlab
OS-level dependencies: mafft (v. 7.490 is included in the package)
License: WTFPL
Version: 0.4.0 (January 2022)

Installation

• The most stable release of uorf4u can be installed directly from pypi:

python3 -m pip install msa4u

• The development version is available at github :

git clone https://github.com/GCA-VH-lab//msa4u.git
cd msa4u
python3 -m pip install --upgrade pip
python3 -m pip install wheel
python3 setup.py sdist bdist_wheel
python3 -m pip install -e .

! If you're a linux user, run msa4u --linux post-install command once to update paths in the premade config files that set by default for MacOS users.

Quickstart guide

Here we present several examples of msa4u vizualisations. The necessary data samples are provided by msa4u at the post-install step:
msa4u --data

Command-line interface

Aligmnent and visualisation.

You can use a fasta file with unaligned sequences as input. In this case, msa4u will use mafft to align your sequences (with --auto parameter: mafft --auto input.fa) and then perform visualisation.

msa4u -fa msa4u_data/aa_sequences.fa

With default parameters you will get alignments file (aa_sequences.aln.fa) and pdf file with visualisaton (aa_sequences.pdf) in your working directory.

Visualisation of a pre-made alignments file

You can use a pre-made alignments file as input with -aln parameter:

msa4u -aln aa_sequences.aln.fa -label description -o visualisation.pdf

In this case we also used optional arguments: -label to set labels style (can be id, description or all - full header of sequences); and -o to set output file name.
See help message for more detailed parameters description (msa4u -h)

Output:

---

API

MSA4u has a simple API allowing it programmatic usage from within a Python program.
Below we descrive several Python snippets that mimic results of command-line calls.

Aligmnent and visualisation

import msa4u

parameters = msa4u.manager.Parameters()
unaligned_fasta_file = "msa4u_data/aa_sequences.fa"
fasta = msa4u.manager.Fasta(fasta=unaligned_fasta_file, parameters=parameters)
mafft_output = fasta.run_mafft()
msa = msa4u.manager.MSA(mafft_output, parameters)
msa.plot()

Visualisation of a pre-made alignments file.

import msa4u

parameters = msa4u.manager.Parameters()
parameters.arguments["label"] = "description"
parameters.arguments["output_filename"] = "visualisation.pdf"

alignments = "aa_sequences.aln.fa"
msa = msa4u.manager.MSA(alignments, parameters)
msa.plot()

Reference

If you find msa4u useful, please cite uorf4u paper. msa4u initially was developed as a sublibrary of uorf4u.
Artyom. A. Egorov, Gemma C. Atkinson, uORF4u: a tool for annotation of conserved upstream open reading frames, bioRxiv 2022.10.27.514069; doi: 10.1101/2022.10.27.514069

Contact

Please contact us by e-mail artemdotegorovATmeddotludotse or use Issues to report any technical problems.

Authors

mas4u is developed by Artyom Egorov at the Atkinson Lab, Department of Experimental Medical Science, Lund University, Sweden. We are open for suggestions to extend and improve msa4u functionality. Please don't hesitate to share your ideas or feature requests.