pangtreebuild 1.0.3

Description:

pangtreebuild 1.0.3

PangtreeeBuild
This repository contains tool for multiple sequence alignment analysis. It implements the idea of pan-genome (Ref. 1) by representing the multialignment as a PO-MSA structure (Partial Order Alignment Graph - Ref. 2). The main purpose of this software is to construct an Affinity Tree - a phylogenetic-like tree, with an agreed sequence (consensus sequence) assigned for each node. The result is saved in JSON file (see its schema in pangtree/pangtreebuild/serialization/affinity_tree_schema.json). Its content can be visualised using PangtreeVis.
This software is a part of the article: P.Dziadkiewicz, N.Dojer 'Getting insight into the pan-genome structure with Pangtree' that will be published soon in BMC Genomics.
Getting Started
Prerequisites
Running:

Python 3.8
BioPython
numpy
jsonpickle
networkx

Testing:

DDT

Installing
pip install pangtreebuild

Quick installation check
This line builds a pan-genome model for an example alignment of 160 Ebola virus sequences and saves it to a JSON file.
python3 -m pangtreebuild --multialignment example_data/Ebola/multialignment.maf
Usage

Import package pangtreebuild to your Python program and use it according to the documentation.

or

Use pangtreebuild via command line with following arguments:

python3 -m pangtreebuild [args]



Name
CLI
Required
Description




Arguments affecting PO-MSA construction:





MULTIALIGNMENT
--multialignment
Yes
Path to the mulitalignment file (.maf or .po)


METADATA
--metadata
No
Optional information about sequences in csv format. The only required column: 'seqid' and its value must match multialignment files identifiers as described in Sequence Naming Convention (below). Example: example_data/Ebola/metadata.csv


RAW_MAF
--raw_maf
No, default=False
Build PO-MSA without transforming multialignment (MAF file) to DAG. PO-MSA built in this way does not reflect real life sequences.


FASTA_PROVIDER
--fasta_provider
No
Nucleotides source if any residues are missed in the multialignment file. Possible values: 'ncbi', 'file'. If not specified: MISSING_NUCLEOTIDE is used.


MISSING_SYMBOL
--missing_symbol
No, default='?'
Symbol for missing nucleotides used if no FASTA_PROVIDER is given.


CACHE
--cache
No
If set, sequences downloaded from NCBI are stored on local disc and reused between program calls, used if FASTA_PROVIDER is 'ncbi'


FASTA_PATH
-fasta_path
Yes if FASTA_PROVIDER='FILE'
Path to fasta file or zipped fasta files with whole sequences present in multialignment, used if FASTA_PROVIDER is 'FILE'.


Arguments affecting Affinity Tree construction:





AFFINITY
-affinity
No
Possible values: 'TREE' (default algorithm, descibed in Documentation.md), 'POA' (simplified version, based solely on Ref. 2)


BLOSUM
--blosum
No, default=bin\blosum80.mat
Path to the blosum filem. Blosum file must include MISSING_NUCLEOTIDE.


HBMIN
--hbmin
No, default=0.9
'POA' parameter. The minimum value of sequence compatibility to generated consensus.


STOP
--stop
No, default=0.99
'TREE' parameter. Minimum value of compatibility in tree leaves.


P
-p
No, default=1
'TREE' parameter. It changes the linear meaning of compatiblities during cutoff finding because the compatibilities are raised to the power o P. For P from range [0,1] it decreases distances between small compatibilities and increases distances between the bigger ones. For p > 1 it increases distances between small compatibilities and decreases distances between the bigger ones.


Arguments affecting output generation:





OUTPUT_DIR
--output_dir, -o
No, default=timestamped folder in current working directory
Output directory path.


OUTPUT_FULL
--output_full
No, default=False
Set, if list of pangenome nodes for sequences and consensuses should be included in pangenome.json.


VERBOSE
--verbose, -v
No, default=False
Set if detailed log files must be produced.


QUIET
--quiet, -q
No, default=False
Set to turn off console logging.


FASTA
--output_fasta
No, default=False
Set to create fasta files with consensuses.


PO
-output_po
No, default=False
Set to create po file with multialignment (without consensuses).



Sequence Naming Convention
[seqid].[anything after first dot is ignored]
Example use cases

Build PO-MSA using default settings (transform to DAG, download missing nucleotides from NCBI) and save to .po file :

python -m pangtreebuild --multialignment example_data/Ebola/multialignment.maf -po


will produce:

pangenome.json
poagraph.po


Generate Affinity Tree, use metadata, detailed logging and default algorithm settings.

python3 -m pangtreebuild --multialignemnt example_data/Ebola/multialignment.maf -metadata example_data/Ebola/metadata.csv -affinity tree -v

will produce:

pangenome.json
details.log
affinitytree/

tresholds.csv
.po files from internal calls to poa software



Tests
python3 -m unittest discover -s pangtreebuild -p tests_*

or
nosetests pangtreebuild

Authors
This software is developed with support of OPUS 11 scientific project of National Science Centre: Incorporating genomic variation information
into DNA sequencing data analysis
License
This project is licensed under the MIT License - see the LICENSE.md file for details
Bibliography


Computational pan-genomics: status, promises and challenges
The Computational Pan-Genomics Consortium. Briefings in Bioinformatics, Volume 19, Issue 1, January 2018, Pages 118–135.


Generating consensus sequences from partial order multiple sequence alignment graphs C. Lee, Bioinformatics, Volume 19, Issue 8, 22 May 2003, Pages 999–1008