pipelign

Built from makenew/python-package.

Description

A pipeline for automated multiple sequence alignment, particularly of viral sequences.

Citation

Pipelign: an alignment pipeline for viral sequences. A.S.Md.M. Hossain and S.D.W.Frost, in preparation.

Usage

usage: pipelign [-h] -i INFILE -o OUTFILE [-t LENTHR] [-a {dna,aa,rna}] [-f]
                [-b] [-z] [-p SIMPER] [-r {J,G}] [-e {P,C}] [-q THREAD]
                [-s MITERATELONG] [-m MITERATEMERGE] -d OUTDIR [-c]
                [-w AMBIGPER] [-n {1,2,3,4,5,6}] [-x]

Pipelign: creates multiple sequence alignment from FASTA formatted sequence file

optional arguments:
  -h, --help            show this help message and exit
  -i INFILE, --inFile INFILE
                        Input sequence file in FASTA format
  -o OUTFILE, --outFile OUTFILE
                        FASTA formatted output alignment file
  -t LENTHR, --lenThr LENTHR
                        Length threshold for full sequences (default: 0.7)
  -a {dna,aa,rna}, --alphabet {dna,aa,rna}
                        Input sequences can be dna/rna/aa (default: dna)
  -f, --keepOrphans     Add fragments without clusters
  -b, --keepBadSeqs     Add long sequences with too many ambiguous residues
  -z, --mZip            Create zipped intermediate output files
  -p SIMPER, --simPer SIMPER
                        Percent sequence similarity for clustering (default: 0.8)
  -r {J,G}, --run {J,G}
                        Run either (J)oblib/(G)NU parallel version (default: G)
  -e {P,C}, --merge {P,C}
                        Merge using (P)arallel/(C)onsensus strategy  (default: P)
  -q THREAD, --thread THREAD
                        Number of CPU/threads to use (default: 1)
  -s MITERATELONG, --mIterateLong MITERATELONG
                        Number of iterations to refine long alignments (default: 1)
  -m MITERATEMERGE, --mIterateMerge MITERATEMERGE
                        Number of iterations to refine merged alignment (default: 1)
  -d OUTDIR, --outDir OUTDIR
                        Name for output directory to hold intermediate files
  -c, --clearExistingDirectory
                        Remove files from existing output directory
  -w AMBIGPER, --ambigPer AMBIGPER
                        Proportion of ambiguous characters allowed in the long sequences (default: 0.1)
  -n {1,2,3,4,5,6}, --stage {1,2,3,4,5,6}
                        1  Make cluster alignments and HMM of long sequences
                        2  Align long sequences only
                        3  Assign fragments to clusters
                        4  Make cluster alignments with fragments
                        5  Align all sequences
  -x, --excludeClusters
                        Exclude clusters from final alignment

In addition, a utility to convert GenBank files into plain FASTA files with the accession as header is included as gb2fas.

Dependencies

• MAFFT
• HMMER3
• CD-HIT
• IQTREE
• BLAST

These can be installed e.g. using conda from the bioconda channel. pipelign has been tested with Python 3.10.

$ conda create -n pipelign -c bioconda -c conda-forge python==3.10
$ conda activate pipelign
$ conda install joblib six parallel blast iqtree mafft cd-hit hmmer -c bioconda -c conda-forge

Installation with pip

Install it directly using pip (using the above environment) with

$ git clone https://github.com/asmmhossain/pipelign
$ cd pipelign
$ pip install .

Installation with setuptools

$ python3 setup.py install

Development and Testing

Source Code

The pipelign source is hosted on GitHub. Clone the project with

$ git clone https://github.com/asmmhossain/pipelign.git

Requirements

You will need Python 3 with pip.

Install the development dependencies with

$ pip install -r requirements.devel.txt

Building a conda package

Installation with conda

First create an environment.

$ conda create -n pipelign python=3.10

Activate the environment.

$ source activate pipelign

Install conda-build:

$ conda install conda-build

Run conda.

$ conda-build . -c bioconda

Tests

Lint code with

$ python setup.py lint

Run tests with

$ python setup.py test

Contributing

Please submit and comment on bug reports and feature requests.

To submit a patch:

1. Fork it (https://github.com/asmmhossain/pipelign/fork).
2. Create your feature branch (git checkout -b my-new-feature).
3. Make changes. Write and run tests.
4. Commit your changes (git commit -am 'Add some feature').
5. Push to the branch (git push origin my-new-feature).
6. Create a new Pull Request.

License

This Python package is licensed under the MIT license.

Warranty

This software is provided "as is" and without any express or implied warranties, including, without limitation, the implied warranties of merchantibility and fitness for a particular purpose.