pyblastbio 0.2.7

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pyblast

This is a wrapper for other applications to run blast searches on SeqRecord objects and JSON objects. Features include:

• Blast self installation
• Alignment to circular queries, using either linear or circular subjects

Installation

You can install BLAST to the pyblast directory using the following command:

pyblast install

This will install it to pyblast/blast_bin. If you want BLAST installed somewhere else, move the ncbi-blast-X.X.X+ folder to your desired location and add path/to/ncbi-blast-X.X.X+/bin to you $PATH. PyBlast will prefer to use the blast stored in your executable path. If it cannot find a blast executable there, it looks for it in that paths in the pyblast/blast_bin/_paths.txt. file. _paths.txt is automatically updated when you run install_blast.py so theres no need to manage the paths manually.

After installing and verifying the blastn command works from the cmd line,

pip install pyblastbio

Usage

This package is a python wrapper for the BLAST command line, intended to be run along with a microservice (e.g. Flask). This package also includes a basic python-based installation script which is used in unit-testing.

Input options

from pyblast import BioBlast
from Bio.SeqRecord