pyabpoa 1.0.0a1

pyabpoa: SIMD-based partial order alignment using adaptive band

pyabpoa: abPOA Python interface

Introduction

pyabpoa provides an easy-to-use interface to abPOA.

Installation

Install pyabpoa with pip

pyabpoa can be installed with pip:

pip install pyabpoa

Install pyabpoa from source

Alternatively, you can install pyabpoa from source:

git clone https://github.com/yangao07/abPOA.git
cd abPOA
make install_py

Getting started

After installation, you can run the toy example script to test it:

python ./python/example.py

Usage

import pyabpoa as pa
a = pa.msa_aligner()
seqs=[
'CCGAAGA',
'CCGAACTCGA',
'CCCGGAAGA',
'CCGAAGA'
]
res=a.msa(seqs, out_cons=True, out_msa=True, out_pog='pog.png') # perform multiple sequence alignment 
                                                                # generate a figure of alignment graph to pog.png

for seq in res.cons_seq:
    print(seq)  # print consensus sequence

res.print_msa() # print row-column multiple sequence alignment in PIR format

APIs

Class pyabpoa.msa_aligner

pyabpoa.msa_aligner(aln_mode='g', ...)

This constructs a multiple sequence alignment handler of pyabpoa, it accepts the following arguments:

• aln_mode: alignment mode. 'g': global, 'l': local, 'e': extension; default: 'g'
• match: match score; default: 2
• gap_open1: first gap opening penalty; default: 4
• gap_ext1: first gap extension penalty; default: 2
• gap_open2: second gap opening penalty; default: 24
• gap_ext2: second gap extension penalty; default: 1
• extra_b: first part of extra band width; default: 10
• extra_f: second part of extra band width; Total extra band width: b+f*L, L is the sequence lengthl default : 0.01
• is_diploid: set as 1 if input is diploid datal default: 0
• min_freq: minimum frequency of each consensus to output for diploid datal default: 0.3

pyabpoa.msa_aligner.msa(seqs, out_cons, out_msa, out_pog=None)

This method performs mutliple sequence alignment and generates

• consensus sequence if out_cons is set as True
• row-column multiple sequence alignment in PIR format if out_msa is set as True
• plot of alignment graph if out_pog is set as a file name with suffix as .png or .pdf

Class pyabpoa.msa_result

pyabpoa.msa_result(seq_n, cons_n, cons_len, ...)

This class describes the information of the generated consensus sequence and row-column multiple sequence alignment. The returned result of pyabpoa.msa_aligner.msa() is an object of this class and it has the following properties:

• seq_n: number of input sequences
• cons_n: number of generated consensus sequences
• cons_len: an array of consensus sequence length
• cons_seq: an array of consensus sequence
• msa_len: size of each row in the row-column multiple sequence alignment
• msa_seq: an array containing seq_n rows of the row-column multiple sequence alignment

pyabpoa.msa_result() also has a function of print_msa. It prints the row-column multiple sequence alignment.