A3M / A2M input for BioPython

This module enables BioPython to parse the Soeding lab's custom HH-suite alignment formats A3M and A2M. The goal of the module is to replicate the results of the reformat.pl included in the HH-suite as faithfully as possible

Installation

pip install A3MIO

Usage

Simply import A3MIO in addition to your BioPython modules. This creates support for the following new formats in both SeqIO and AlignIO packages:

• a3m - A3Ms with insertions
• a3m-nogaps A3Ms that ignore insertions w.r.t. query sequence
• a2m - A2Ms with insertions
• a2m-nogaps A2Ms that ignore insertions w.r.t. query sequence

Example:

import Bio.SeqIO
import A3MIO

for record in Bio.SeqIO.parse("example.a3m", "a3m"):
	print(record)

Status

Not yet tested on larger sequence databases for accuracy or performance. Be sure to evaluate before you use it :)

License

GNU GPL v3